key: cord-282177-8l7zukg4 authors: lin, yi-chun; cheng, chien-yu; cheng-pin, chen; cheng, shu-hsing; chang, sui-yuan; hsueh, po-ren title: a case of transient existence of sars-cov-2 rna in the respiratory tract with the absence of anti-sars-cov-2 antibody response date: 2020-05-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.070 sha: doc_id: 282177 cord_uid: 8l7zukg4 abstract we report a patient who had travelled to japan presented mild respiratory symptom during the covid-19 infection outbreak period. there was transient existence of sars-cov-2 rna in his oropharynx. the rna was absent in the six respiratory specimens that were subsequently tested. anti-sars-cov-2 antibody response in the acute and convalescent sera were absent. the reported case indicates that transient colonization of sars-cov-2 in the upper respiratory tract is possible without inciting any antibody response against the virus. early diagnosis of covid-19 is essential for containing and mitigating sars a 30-year-old man, an engineer, presented to our hospital on february 27, 2020, with a mild cough since february 24, 2020 (day 1 of illness informed consent was obtained from the patient for publication of this case report. no specific funding was received for this work. the authors declare no competing interests ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. hydroxychloroquine and azithromycin as a treatment of covid-19: results of an open-label non-randomized clinical trial clinical characteristics of coronavirus disease 2019 in china asymptomatic carrier state, acute respiratory disease, and pneumonia due to severe acute respiratory syndrome coronavirus 2 (sars-cov-2): facts and myths a case of covid-19 and pneumonia returning from macau in taiwan: clinical course and anti-sars-cov-2 igg dynamic dynamics of anti-sars-cov-2 igm and igg antibodies among covid-19 patients laboratory diagnosis of emerging human coronavirus infections-the state of the art lymphopenia predicts disease severity of covid-19: a descriptive and predictive study temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study antibody responses to sars-cov-2 in patients of novel coronavirus disease 2019 key: cord-260332-tnz6k2z1 authors: tran, tu anh; cezar, renaud; frandon, julien; kabani, sarah; corbeau, pierre title: ct scan does not make a diagnosis of covid-19: a cautionary case report() date: 2020-09-02 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.073 sha: doc_id: 260332 cord_uid: tnz6k2z1 here, we report the clinical case of a 12-year-old girl presenting with flu-like symptoms, cough, anosmia, ageusia, breathing difficulties, patchy ground glass opacities on tdm chest scan who turned out to be coronavirus 229e-infected. this case must draw attention on the risk of false covid-19 diagnosis when relying overly on ct scan imaging. rt-pcr assays of nasopharyngeal samples at admittance and 24 hours later, were negative for sars-cov-2. multiplex pcr on rhynopharyngeal secretions was positive for coronavirus 229e. the patient responded favourably to treatment with 60 mg prednisolone and 5mg salbutamol in aerosol every two hours, which was progressively spaced out. the fever did not return, although the productive cough remained, and the patient was discharged two days after admittance. in this case report, parents' anosmia and ageusia as well as chest scanner could have been misleading. anosmia has been described for coronaviruses different from sars-cov-2 1 . according to kim et al., scanner screening of patients with suspected covid-19 in low-prevalence countries has a poor positive prediction value (1%-31%) 2 . basing covid-19 diagnosis strictly on clinical signs and imaging may lead to false positive diagnosis, resulting in inappropriate medical care and errors in contact tracing. the study was carried out in accordance with the french guidelines and regulations. this work has been funded by the university hospital of nîmes, france. olfactory neuropathy in severe acute respiratory syndrome: report of a case diagnostic performance of ct and reverse transcriptase-polymerase chain reaction for coronavirus disease 2019: a meta-analysis. radiology the authors declare that they have no conflict of interest. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-254776-m4makxr8 authors: luo, shiua; guo, yanrong; zhang, xiaochun; xu, haibo title: a follow-up study of recovered patients with covid-19 in wuhan, china date: 2020-06-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.119 sha: doc_id: 254776 cord_uid: m4makxr8 nan the 2019 novel coronavirus disease (covid-19) epidemic has clearly entered a new stage with rapid spread in countries outside china [1] . it has been declared a pandemic by the world health organization. the chinese government has taken serious actions and made unremitted efforts in prevention and control of covid-19 epidemic, including imposing quarantines and travel restrictions on an unprecedented scale and investing a huge amount of medical resources [2] . currently, a large number of covid-19 patients in wuhan have been cured and discharged. in wuhan, china, all cured patients with covid-19 are required to quarantine in either a designated hotel room or at home for 14 days [3] . they will return to normal j o u r n a l p r e -p r o o f social life after a follow-up by strictly eliminating the recurrence of covid-19. they will receive follow-up check-ups in a designated fever clinic, including physical examination, laboratory test including igg and igm antibody, c-reactive protein，the level of leukocyte and lymphocyte, and chest ct scan. at present, the outcome of these patients is not yet fully clear. we retrospectively evaluated the data of the recovered patients with covid-19 in two different designated fever clinics in wuhan, with a goal to provide relevant information about these patients. in this study, only 7.7‰ patients experienced recurrence during isolation and observation, and all presented with mild symptoms. no nosocomial transmission was found in this process. serological tests to identify antibodies played a key role in surveillance of recurrence of covid-19 [4] . the studies about viral shedding in discharged patients need further investigation. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. sars-cov-2 viral load in upper respiratory specimens of infected patients who. report of the who-china joint mission on coronavirus disease 2019 (covid-19) there is no funding source of this study.this study was approved by the medical ethical committee of zhongnan hospital of wuhan university. key: cord-029882-kufs0fxe authors: malviya, amit title: the continued dilemma about usage of hydroxychloroquine: respite is in randomized control trials date: 2020-07-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.054 sha: doc_id: 29882 cord_uid: kufs0fxe nan is notable that in the present study, concomitant use of steroid in patients receiving hydroxychloroquine, was more than non-treated group. so, in absence of this critical information about the duration between the onset of symptoms and administration of first dose of hcq, it seems difficult to interpret that the positive effects were due to hcq or steroids. hcq is touted for treatment of covid 19 primarily based on its anti-viral properties, thus the timing of administration becomes very important for a meaning full assessment of study results. secondly, hcq concentrates in lungs after initial doses 3 and that is the time when its effect is supposed to be maximum. administration of hcq late in the course of disease may not be that effective. thirdly, they utilised maximal modified sequential organ failure assessment (msofa )scores for classifying patient severity of disease . recently it been shown that this score is not accurate for predicting severity of disease in covid 19 patients . 4 fourthly , a qtc interval-based algorithm specifically designed to ensure the safe use of hydroxychloroquine was utilised . this is a very safe practice but it might have resulted in exclusion of high cardiac risk patients . covid 19 is a multisystem disease and the disease itself promotes proarrhythmic milieu with prolonged qt intervals at baseline .5,6 risk assessment of hcq therapy is not complete if such patients are excluded. finally , mechanism of action of hcq against is a part of its broad anti-viral and immunomodulatory properties and no specific pharmacologic actions are described for sars-cov-2 infection. 7, 8 majority of publications in the recent times on hcq , for usage in covid 19, are limited by low methodical quality and by and large have shown negative or neutral results . 9,10 weather hcq as initial anti-viral agent prevents progression to severe disease is not known clearly . in severe disease with multi system involvement and pro arrhythmic milieu covid-19: immunopathology and its implications for therapy pharmacologic treatments for coronavirus disease 2019 (covid-19): a review mechanisms of action of hydroxychloroquine and chloroquine: implications for rheumatology critically ill sars-cov2-infected patients are not stratified as sepsis by the qsofa chloroquine and hydroxychloroquine in covid-19 ventricular arrhythmia risk due to chloroquine / hydroxychloroquine treatment for covid-19: should it be given in vitro antiviral activity and projection of optimized dosing design of hydroxychloroquine for the treatment of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) effects of chloroquine on viral infections: an old drug against today's diseases? the lancet. infectious diseases the urgency of care during the covid-19 pandemic -learning as we go covid-19 coronavirus research has overall low methodological quality thus far: case in point for chloroquine/hydroxychloroquine key: cord-258881-74aijckl authors: wang, maomao; luo, limin; bu, haiji; xia, hu title: case report: one case of coronavirus desease 2019(covid-19) in patient co-nfected by hiv with a low cd4+ t cell count date: 2020-04-23 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.060 sha: doc_id: 258881 cord_uid: 74aijckl abstract the ongoing outbreak of covid-19 that began in wuhan, china has become an emergency of international concern when thousands of peolple were infected around the world.we report a case infected by sars-cov-2 and hiv simultaneously,which showed a longer course of disease and slower generation of specific antibody. this case highlights the coinfection of sars-cov-2 and hiv may impaire the immune system worse. since december 2019, an outbreak of coronavirus disease, officially named by the world health organization as covid-19, appeared in pneumonia and respiratory illness. lymphopenia has been considered as a poor prognostic factor for severe acute respiratory syndrome(sars) [1] as well as in covid-19 [2] . here, we report clinical findings in a patient confirmed with covid-19, who was also co-infected by human immunodeficiency virus (hiv) . here we report a patient infected by sars-cov-2 , who had a relatively long course of disease with unstable state. then eight markers of infectious diseases was checked and the result showed that abtibodies to hiv and syphilis were positive .then the patient was transferred to specialty hospital for further treatment on march 8. in the specialty hospital, the cd4 cell count was 34/ul, cd8 cell count was 737/ul and cd4/cd8 was 0.05. the dectection of cryptococcus antigen in serum was negative and the patient was then given anti-hiv treatment . on february 11, 2020, a 37-year-old man was presented to wuhan huo shen shan hoapital, with a history of fever, dry cough and chest pain since january 10, 2020. the chest ct of this patient on covid-19 is caused by a novel type of coronavirus sars-cov-2. people are generally susceptible to sars-cov-2 infection, especially the elderly patients and those with underlying diseases [2] . the median time from onset of symptoms to first hospital admission was 7 days, to shortness of breath was 8 days, to ards was 9days, to mechanical ventilation was 10.5 days, and to icu admission was 10.5 days. [3] the patient described here were admitted to our hospital because of fever which lasting nearly one month and typical changes of viral pneumonia in lung ct imaging. the prominent complaint was dyspnea, the study of qin showed, the total number of b cells, t cells, and nk cells significantly decreased in patients with covid-19, and more evident in the severe cases compared to the non-severe group. the author suggested that sars-cov-2 might damage lymphocytes, especially t lymphocytes, and the immune system was impaired during the period of disease [2] . corticosteroids may delay viral clearance [3] . in this case, corticosteroid therapy was used( methylprednisone 200mg totally) accompanied with arbidol for anti-virus therapy.the body temperature turned normal. we also used tocilizumab one time to fight inflammation storm, which did not show the reduction of il-6 in serum. in conclusion, we report the clinical features of a patient infected by sars-cov-2 and hiv. the case appeared to be a long course of disease for more than 2 months. and until the later period of the course the igm in serum could be detected, which may due to the destroy of the immune response by the two viruses cooperatively. the epidemiology of severe acute respiratory syndrome in the 2003 hong kong epidemic:an analysis of all 1755 patients dysregulation of immune response in patients with covid-19 in wuhan we declare that we have no financial and personal relationships with other people or organizations that can inappropriately influence our work, there is no professional or other personal interest of any nature or kind in any product, service and/or company that could be construed as influencing the position presented in, or the review of, the manuscript entitled. key: cord-268037-szhzmzys authors: eshaghi, a.; blair, j.; burton, l.; lombos, e.; choi, k.; de lima, c.; drews, s.j. title: a paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with h274y-positive influenza a (h1n1) strains date: 2008-12-17 journal: int j infect dis doi: 10.1016/j.ijid.2008.07.026 sha: doc_id: 268037 cord_uid: szhzmzys nan a paucity of co-infecting respiratory viral pathogens in nasopharyngeal specimens from patients infected with h274y-positive influenza a (h1n1) strains the h274y mutation in the neuraminidase gene of influenza a (h1n1) has been associated with oseltamivir resistance. 1 initial evaluations of this mutation in animal models suggested that this mutation had reduced fitness and reduced pathogenicity when compared to corresponding wild-type viruses. 2,3 earlier reports of clinical infections supported this view and h274y was rarely reported. 4 however, in the last year, there have been reports of dramatic increases in the proportion of h274y mutations identified in clinical isolates throughout the world. 5 if pathogenicity was indeed compromised in these most recent mutants, then it should be determined whether patients infected with oseltamivirresistant strains are presenting with illness associated with another co-infecting respiratory viral pathogen. the purpose of this brief investigation was to determine whether nasopharyngeal specimens from patients infected with strains of influenza a (h1n1) carrying the h274y mutation were more likely than not to contain other commonly circulating respiratory viral pathogens. nasopharyngeal specimens from patients with influenzalike illness were sent to the ontario public health laboratories. isolates of influenza a collected from toronto, ontario, canada (estimated population 2.7 million) during the period november 14, 2007 to february 14, 2008 were screened by reverse transcriptase (rt)-pcr for the h1n1 subtype using primers described previously. 6 strains of isolates were confirmed by sanger sequencing and sequence alignment. neuraminidase gene sequencing was undertaken and sequences were aligned using clustalx. isolate sequences were compared to sequences with described h274y mutations: genbank accession no. 7 specimens corresponding to h274y mutant and h274 wild-type isolates were blinded and chosen at random for a retrospective investigation for other respiratory viral pathogens (adenovirus, coronavirus 229e/nl63, coronavirus oc43, influenza a/b, parainfluenza virus 1/2/3, respiratory syncytial virus a/b, rhinovirus a) using the seeplex 1 rv detection kit protocol (seegene, inc., rockville, md). 8 data analysis was carried out using graphpad prism 5 (graphpad software, inc., la jolla, ca, usa). all influenza a (h1n1) isolates resembled most closely influenza a/solomon islands/03/06 (h1n1). of the 19 specimens containing the h274y mutation, none contained any other respiratory viral pathogen that could be detected by the seeplex rv detection kit protocol. however, two of 40 specimens (5%) containing wild-type h274 influenza a (h1n1) were also positive for parainfluenza virus 2 and one specimen (2.5%) was positive for respiratory syncytial virus b. statistical analysis indicated that there was no difference between h274y mutant and h274 wild-type groups in the proportion of specimens carrying other respiratory viral pathogens (fisher's exact test, p = 0.5). until the pathogenicity of oseltamivir-resistant influenza a viruses is understood better, infections with these viruses should be taken seriously by both clinicians and public health workers. 9 the detection of influenza and the lack of other respiratory viral pathogens detected in the h274y mutant group suggest that illness in these patients could only be associated with influenza and not any other of the more common respiratory viral pathogens. however, it should be noted that the interaction of influenza a and bacterial pathogens could not be determined in these specimens given issues of specimen collection and data collection. given the lack of data supporting a co-infection model, it is considered that further work must be undertaken to determine the fitness and virulence of the h274y mutant influenza a strains circulating currently. conflict of interest: no competing interests declared. mechanism by which mutations at his274 alter sensitivity of influenza a virus n1 neuraminidase to oseltamivir carboxylate and zanamivir influenza viruses resistant to the antiviral drug oseltamivir: transmission studies in ferrets the h274y mutation in the influenza a/h1n1 neuraminidase active site following oseltamivir phosphate treatment leave virus severely compromised both in vitro and in vivo detection of human influenza a (h1n1) and b strains with reduced sensitivity to neuraminidase inhibitors european centre for disease prevention and control. emergence of seasonal influenza viruses type a (h1n1) with oseltamivir resistance in some european countries at the start of the 2007-2008 influenza season. 1-11 application of a fluorogenic pcr assay for typing and subtyping of influenza viruses in respiratory samples neuraminidase subtyping of human influenza a viruses by rt-pcr and its application to clinical isolates comparison of the seeplex reverse transcription pcr assay with the r-mix viral culture and immunofluorescence techniques for detection of eight respiratory viruses emergence of drug-resistant influenza virus: population dynamical considerations key: cord-274230-old0xmcc authors: zhao, qianwen; meng, meng; kumar, rahul; wu, yinlian; huang, jiaofeng; deng, yunlei; weng, zhiyuan; yang, li title: lymphopenia is associated with severe coronavirus disease 2019 (covid-19) infections: a systemic review and meta-analysis date: 2020-05-04 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.086 sha: doc_id: 274230 cord_uid: old0xmcc abstract objectives coronavirus disease 2019 (covid-19) is a new respiratory and systemic disease which needs quick identification of potential critical patients. this meta-analysis aimed to explore the relationship between lymphocyte count and the severity of covid-19. methods comprehensive systematic literature search was carried out to find studies published from december 2019 to 22 march 2020 from five databases. the language of literatures included english and chinese. mean difference (md) of lymphocyte count in covid-19 patients with or without severe disease and odds ratio (or) of lymphopenia for severe form of covid-19 was evaluated with this meta-analysis. results overall 13 case-series with a total of 2282 cases were included in the study. the pooled analysis showed that lymphocyte count was significantly lower in severe covid-19 patients (md -0.31×109/l; 95%ci: -0.42 to -0.19×109/l). the presence of lymphopenia was associated with nearly threefold increased risk of severe covid-19 (random effects model, or=2.99, 95% ci: 1.31-6.82). conclusions lymphopenia is a prominent part of severe covid-19 and a lymphocyte count of less than 1.5×109/l may be useful in predicting the severity clinical outcomes. microsoft excel was used to analyze the clinical symptoms and the laboratory results. a meta-analysis was carried out using r software (version 3.6.3, available on 125 https://www.r-project.org). heterogeneity among studies was tested using the cochran 126 chi-square test and i 2 , when i 2 < 50%, a fixed-effects model was used, while when 127 i 2 > 50%, a random-effects model was selected. if statistical heterogeneity was found 128 among the results, a further sensitivity analysis was conducted to determine the source 129 of heterogeneity. after the significant clinical heterogeneity was excluded, the 130 randomized effects model was used for meta-analysis. funnel plot were used to detect 131 publication bias. p <0.05 was considered as statistical significance. five studies reported the relationship between lymphopenia and the severity of 170 covid19[11, 12, 15, 18, 19] . lymphopenia was defined as a lymphocyte count of 171 less than 1.1×10 9 /l in four studies [11, 12, 16, 18] , and as less than 1.5×10 9 /l in 172 one [19] . the pooled or as summarized in figure 2c shows that the presence of after excluding this study, the i 2 of heterogeneity reduced to 48%, the or of 178 lymphopenia was 2.17 (95% ci: 1.0126-4.6812). the funnel plot indicated no 179 publication bias inside this study ( figure 2d ). in addition, another drawback of our study is that there is no data relating to from sars to covid-19: a previously unknown sars-related 258 coronavirus (sars-cov-2) of pandemic potential infecting humans -call for a one health approach one health the continuing 2019-ncov epidemic threat of novel 261 coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china severe outcomes among patients with coronavirus disease 2019 (covid-19) -united states the sars-cov-2 outbreak: what we know the impact of copd and smoking history on the severity of covid-19: a systemic review and meta-analysis coronavirus disease 2019: what we know functional exhaustion of antiviral lymphocytes in covid-19 molecular characterization of hepatitis c 273 virus in end-stage renal disease patients under hemodialysis clinical features and treatment analysis of 79 coronovirus infected 276 pneumonia diagnostic utility of clinical laboratory data determinations for 278 patients with the severe covid-19 analysis of factors associated with disease outcomes in hospitalized 280 patients with 2019 novel coronavirus disease clinical and biochemical indexes from 2019-ncov infected patients 282 linked to viral loads and lung injury risk factors associated with acute respiratory distress syndrome 284 and death in patients with coronavirus disease clinical characteristics of 138 hospitalized patients with clinical features of 69 cases with coronavirus disease 289 clinical course and outcomes of critically ill patients with sars-cov-2 291 pneumonia in wuhan, china: a single-centered, retrospective, observational study. the lancet 292 respiratory medicine clinical course and risk factors for mortality of adult inpatients with clinical characteristics of coronavirus disease retrospective study on the epidemiological 300 characteristics of 139 patients with novel coronavirus pneumonia on the effects of severity clinical features of patients infected with a major outbreak of severe acute respiratory syndrome in hong kong clinical features and short-term outcomes of 144 307 patients with sars in the greater toronto area hematological findings in sars patients and possible mechanisms 309 (review) effects of severe acute respiratory syndrome (sars) coronavirus 311 infection on peripheral blood lymphocytes and their subsets elevated exhaustion levels and reduced functional diversity 313 of t cells in peripheral blood may predict severe progression in covid-19 patients functional exhaustion of antiviral lymphocytes in covid-19 covid-19, cytokines and immunosuppression: what can 318 we learn from severe acute respiratory syndrome? insight into 2019 novel coronavirus -an updated interim review and lessons from lymphopenia predicts disease severity of covid-19: a 322 descriptive and predictive study acknowledgments: not applicable. key: cord-272015-1anph6qi authors: dauby, nicolas; bottieau, emmanuel title: the unfinished story of hydroxychloroquine in covid-19: the right anti-inflammatory dose at the right moment? date: 2020-10-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.032 sha: doc_id: 272015 cord_uid: 1anph6qi nan dear editor, uncontrolled inflammation, partly related to activated macrophages, is widely recognized as an independent cause of clinical deterioration and mortality in hospitalised patients (webb et al.; del valle et al. 2020) . following the results of the recovery trial and of an additional meta-analysis, corticosteroids are now recommended as a standard of care for hospitalized patients with severe and critical covid-19 (who 2020). importantly, the benefit of this anti-inflammatory intervention has been observed with a low dose of dexamethasone, while observational studies using higher dosage of corticosteroids have not reported any favourable effect on mortality (hasan et al. 2020) . the observation by lammers et al (lammers et al.) that early hcq treatment after admission at low dosage (2400 mg in total) is associated with lower risk of admission in intensive care unit coincides with large observational studies showing a lower mortality rate in patients exposed to hcq therapy compared to no or other treatment. of note, in all these studies and in contrast to the recovery trial, low doses of hcq (< 2.5 gr. in total) were used, often soon after admission (arshad et al. 2020; ayerbe et al. 2020; catteau et al. 2020; covid-19 risk and treatments (corist) collaboration 2020). another recent large cohort study of patients on low-dose hcq for inflammatory disorders reported an association between chronic hcq use and reduced mortality following sars-cov-2 infection (gentry et al. 2020) . as highlighted by the findings of lammers et al, the timing of hcq therapy (administration within 1 day of admission) could explain discrepancies between different studies. in the recovery trial, the median time between symptoms onset and randomization was 9 days j o u r n a l p r e -p r o o f and a substantial proportion of patients (16.7%) was already on mechanical ventilation at randomization(the recovery collaborative group 2020). hcq has been used as anti-inflammatory drug for decades as therapy of inflammatory disorders and its impact on inflammatory responses is well documented. hcq inhibits the production of the pro-inflammatory cytokines interleukin (il)-6, tnf-α and il-1-β by activated macrophages (sperber et al. 1993; jang et al. 2006) , which are notoriously associated with covid-19 severity (webb et al.; del valle et al. 2020 ) and also the production of chemotactic cytokines involved in the recruitment of pro-inflammatory cells in the lungs(grassin-delyle et al. 2020). in line with this, an italian study suggests that the benefit of hcq was restricted to patients with elevated c-reactive protein levels(covid-19 risk and treatments (corist) collaboration 2020). thrombotic events are another well recognized complication of severe covid-19 (llitjos et al. 2020 ) and the presence of lupus anticoagulant has been reported in hospitalised covid-19 (bowles et al. 2020) . hcq therapy has been associated with a decrease of lupus anticoagulant levels as well as of platelet activation and thrombotic events in lupus patients (broder and putterman 2013) . interestingly, b cell abnormalities similar to those reported in autoimmune disease such as active lupus were reported in patients with severe covid-19 (woodruff et al. 2020 ). hcq has no antiviral activity in vivo against sars-cov-2 as shown in pre-clinical models such as syrian hamsters, non-human primates and human lung cells, and should therefore not be used as antiviral therapy in covid-19 (maisonnasse et al. 2020) . however, to further understand the positive effects observed in large observational studies that used hcq offlabel in the early months of the pandemic, the hypothesis of an anti-inflammatory action j o u r n a l p r e -p r o o f 4 should not be discarded. we suggest that ongoing trials evaluating hcq specifically look at its effect on inflammatory parameters with add-on studies if necessary. in the same line, ongoing trials are investigating colchicine to prevent hospitalisation in sars-cov-2 infected subjects, and the rationale is based on anti-inflammatory properties, that are partly shared treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalized with covid-19 the association of treatment with hydroxychloroquine and hospital mortality in covid-19 patients hydroxychloroquine: from malaria to autoimmunity lupus anticoagulant and abnormal coagulation tests in patients with covid-19 hydroxychloroquine use is associated with lower odds of persistently positive antiphospholipid antibodies and/or lupus anticoagulant in systemic lupus erythematosus low-dose hydroxychloroquine therapy and mortality in hospitalised patients with covid-19: a nationwide observational study of 8075 participants use of hydroxychloroquine in hospitalised covid-19 patients is associated with reduced mortality: findings from the observational multicentre italian corist study an inflammatory cytokine signature predicts covid-19 severity and survival longterm hydroxychloroquine use in patients with rheumatic conditions and development of sars-cov-2 infection: a retrospective cohort study chloroquine inhibits the release of inflammatory cytokines by human lung explants mortality in covid-19 patients with acute respiratory distress syndrome and corticosteroids use: a systematic review and meta-analysis chloroquine inhibits production of tnf-α, il-1β and il-6 from lipopolysaccharide-stimulated human monocytes/macrophages by different modes early hydroxychloroquine but not chloroquine use reduces icu admission in covid-19 patients high incidence of venous thromboembolic events in anticoagulated severe covid-19 patients hydroxychloroquine use against sars-cov-2 infection in non-human primates colchicine as a possible therapeutic option in covid-19 infection selective regulation of cytokine secretion by hydroxychloroquine: inhibition of interleukin 1 alpha (il-1-alpha) and il-6 in human monocytes and t cells effect of hydroxychloroquine in hospitalized patients with covid-19 clinical criteria for covid-19-associated hyperinflammatory syndrome: a cohort study world health organization extrafollicular b cell responses correlate with neutralizing antibodies and morbidity in covid-19 key: cord-279581-d2l4nnex authors: abuhabib, a.a.; abu-aita, said n.; procter, caitlin; al-smeri, ibtesam title: unique situation of gaza strip dealing with covid-19 crisis date: 2020-09-03 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.070 sha: doc_id: 279581 cord_uid: d2l4nnex infected covid19 cases continue to increase, having already reached 21 million globally, attracting scientists around the world to trying to find a possible vaccine. unlike many places around the world, movement restrictions and difficulties in travelling in and out due to 13 years old blockade with no possibility for tourists to travel in, has benefited gaza in terms of being self-isolated and less likely to have many travellers or foreigners carrying the virus and infecting the population. first cases discovered on 22 march 2020 and by 05 july 2020, they were still only 72 cases confirmed, 60 of whom successfully treated, 11 active cases and only 1 death. constructively, this study follows direct observation approach with in-depth disk review for data collected locally from official sources (governmental bodies, un agencies, and ingos), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with covid19 supported by the application of simple risk matrix for each scenario within a limited time frame covering the period from 22 march to 05 july 2020. three different risk scenarios associated with covid19 risks studied and analysed towards understanding exceptional circumstances surrounding gaza along with potential mitigation measures executed and suggested. unlike many other parts of the middle east region, and particularly egypt, israel and the west bank, cases of covid-19 were not detected until 22 march 2020 in the gaza strip. on that particular day, the first two cases for palestinians travelling from pakistan, arriving in gaza through its southern border with egypt, tested positive to the virus [3] . such delay is most likely related to the restricted movement of palestinians to and from gaza, due to the imposed blockade leaving the residents with only two crossing points in the north with israel (eretz) and in the south with egypt (rafah) experiencing sever movement constraints in both crossing points. -stop all educational activities including schools and universities as well as reducing office working hours to the minimum for all non-medical non-security forces public staff. -closure of all wedding halls, stop weekly mobile markets, prohibit all gathering events (e.g. parties, workshops, conferences, etc.) and prevent any form of crowdedness. -encourage all citizens to stay home and limit their movements to the minimum. j o u r n a l p r e -p r o o f 4 as such, this study aims at assessing and analysing the unique situation of gaza (characterized by long lasting blockade with restricted movement, dense population, and political implications) in the light of covid-19 spreading and outlining potential scenarios, both optimistic and pessimistic associated with control measures acting as responsive course of action. this study follows the direct observation approach with in-depth disk review for data collected locally from official sources (governmental bodies, un agencies, and ingos), concrete context analysis is then made and employed towards predicting the potential risk scenarios associated with covid19 supported by the application of simple risk matrix for each scenario likelihood determination and consequences identification within a limited time frame covering the period from 22 march to 05 july 2020. in this study, situation analysis is made based on risk assessment conducting. risk assessment is made by applying risk matrix tool illustrated in figure no.1 and table no.1 [16] towards: assessing potential risks acting as potential scenarios, identifying associated impacts for each risk and suitable mitigation j o u r n a l p r e -p r o o f measures to be considered. the likelihood per each risk assumed is made base on local authorities' mitigation measures taken and impact is similarly identified. obviously, the second scenario has been going for nearly a month now and does not seem to impact the healthcare system badly, as things are under control. however, and despite the fact that such situation seems to be positive on the health side, the restricted measures taken by the local authorities previously mentioned are highly affecting the life of gazans severely, as people are living in an exceptional situation presented by the closure of all education institutes including schools and universities, regular weekly markets are prohibited, public activities and gathering are not allowed, etc. consequently, and due to protective measures taken by local authorities, thousands of daily paid j o u r n a l p r e -p r o o f workers, street vendors, fishermen and farmers, small scale business owners, and others have either lost their income fully or partially or having their livelihoods at high risk. some aids were provided by international organizations and external donors but they are far below population needs. according to the state of emergency palestine's covid response plan announced by palestinian authorities in ramallah, the economic losses across palestinian territories are expected to reach $2.8 billon [17] . it should be taking into account that the second scenario is less likely to develop or to roll over to the first scenario compared to the third one. sustaining this particular scenario may act as an exit strategy where not only the local authorities' measures sustained but also coping mechanisms developed across the past years of isolation and besieged of the population are employed. associated lowincome, restricted movements, low quality public services, sequence of wars and emergency incidences, and other difficulties faced by the population for long time contribute positively to comply smoothly with restricted measures imposed by the authorities to respond to covid19 outbreak perhaps for longer period than any community across the globe withstand. on the other hand, sustaining protective measures associated with the second scenario are highly recommended but the longer they go, the more economic burden is felt by the population. therefore, and based on the situation developing towards covid19 containment in gaza, gradual easing of these measures with close monitoring can be also applied for short-term period while weekly evaluation is to be conducted by authorities. the study does not involve the use of human or animal subjects in any way (e.g. experimental data, interviews, etc.). therefore, medical or helsinki declaration are not required nor needed. the reality of integrating the dimensions of computerized health information systems in dar al-shifa medical complex unocha, health facilities in gaza mosques reopening in gaza risk matrix: an approach for identifying, assessing, and ranking program risks evidence based management guideline for the covid-19 pandemic-review article ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.☐the authors declare the following financial interests/personal relationships which may be considered as potential -no financial interest.-study was not funded by any external or internal party. key: cord-274028-dvsvtsn0 authors: del brutto, oscar h.; costa, aldo f.; mera, robertino m.; recalde, bettsy y.; bustos, javier a.; garcía, héctor h. title: sars-cov-2-related mortality in a rural latin american population date: 2020-08-08 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.003 sha: doc_id: 274028 cord_uid: dvsvtsn0 a sudden increase in adult mortality associated with respiratory diseases was noticed in atahualpa (a rural ecuadorian village), coinciding with the introduction of sars-cov-2 in the region. from a total of 1,852 individuals aged ≥18 years, 40 deaths occurred between january and june, 2020. in addition, a seroprevalence survey showed that 45% of the adult population have sars-cov-2 antibodies. verbal autopsies revealed sars-cov-2 as the most likely cause of death in 29 cases. the mean age of suspected or confirmed sars-cov-2 cases was 76.9 ± 12.1 years, while that of those dying from unrelated causes was 60.3 ± 20.4 years (p = 0.003). the overall mortality rate was 21.6 per 1,000 population (95% c.i.: 15.9 – 29.2), almost three-quarters of it due to sars-cov-2 (15.7 per 1,000; 95% c.i.: 11 – 22.4). this configures a 266% of excess mortality when compared to 5.9 per 1,000 (95% c.i.: 3.3 – 10.6) deaths from other causes. when sars-cov-2 mortality rate was calculated in individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% c.i.: 47.8 – 98.4). after peaking in april and may, mortality significantly decreased. it is possible that the high proportion of infected individuals and the resulting herd immunity contributed to the observed reduction in mortality. the novel coronavirus disease 2019 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), has claimed the lives of more than 600 thousand people [1] . highly prevalent in urban centers of china, usa, and european countries, the disease has spread to africa and latin america, where rural populations are especially j o u r n a l p r e -p r o o f vulnerable because of multiple factors inherent to under-development [2] [3] [4] . despite the vast information on sars-cov-2 published from urban centers, there is little or nil evidence about the mortality rate of individuals with sars-cov-2 in remote rural settings. a sudden increase in adult mortality associated with respiratory diseases was noticed in atahualpa, a rural ecuadorian village (2º18's, 80º46'w), coinciding with the introduction of sars-cov-2 in the region [5] . such deaths started on march 2020, reached a peak on april and may, and subsequently declined during june. here, we report sars-cov-2 mortality rates in atahualpa residents aged ≥18 years. departing from the archives of the atahualpa project, we obtained data from our last census of the adult population, registered deaths occurring during the first semester of 2020, and reported the results of a door-to-door seroprevalence survey conducted during may, 2020 [6] . deaths were classified in sars-cov-2-related and unrelated (based on verbal autopsies and confirmatory tests). verbal autopsies findings were categorized according to world health organization operational definitions for suspected covid-19 case, as follows: 1) acute febrile respiratory illness and exposure of community transmission to covid-19 disease during the 14 days prior to symptom onset; 2) any acute respiratory illness and contact with a confirmed or probable covid-19 case in the last 14 days; and 3) severe acute respiratory illness (fever and at least one sign/symptom of respiratory disease and requiring hospitalization) in the absence of an alternative diagnosis j o u r n a l p r e -p r o o f [7] . mortality rates for the entire cohort and for the subset of older adults (aged ≥60 years) were calculated. a door-to-door survey of atahualpa residents (december, 2019), conducted as part of the atahualpa project cohort study [8] , revealed 1,852 individuals aged ≥18 years, 392 of whom were aged ≥60 years. forty deaths occurred between january and june, 2020. verbal autopsiesprovided by family related households membersrevealed sars-cov-2 as the most likely cause of death in 29 cases [7] , including five confirmed sars-cov-2 deaths (where the individuals had diagnostic tests performed at a local hospital). all the 24 individuals who died with suspected covid-19 disease had fever and respiratory symptoms and entered into who category 2, including 19 who had seropositive household members and five reporting frequent contact with seropositive neighbors. other causes of death (cancer, chronic liver failure, head trauma and suicide) occurred in the remaining 11 cases. in january and february there were four deaths, all unrelated to sars-cov-2. in march, two of four deaths were from suspected sars-cov-2 infection. in april there were 22 deaths, 18 of which were related to suspected or confirmed sars-cov-2 infections, as were seven out of eight deaths in may. the two deaths in june were confirmed sars-cov-2 cases. the mean age of the 29 suspected or confirmed sars-cov-2 cases was 76.9±12.1 years, while that of those dying from unrelated causes was 60.3±20.4 years (p=0.003). twenty-j o u r n a l p r e -p r o o f seven out of the 29 deaths likely related to sars-cov-2 were individuals aged ≥60 years, as were seven out of 11 deaths from unrelated causes (p=0.039). the overall mortality rate in atahualpa residents aged ≥18 years was 21.6 per 1,000 population (95% c.i.: 15.9 -29.2), almost three-quarters of it due to sars-cov-2 (15.7 per 1,000; 95% c.i.: 11 -22.4 ). this configures a 266% of excess mortality when compared to 5.9 per 1,000 (95% c.i.: 3.3 -10.6) deaths from other causes. when sars-cov-2 mortality rate was calculated in the subset of individuals aged ≥60 years, it raised up to 68.9 per 1,000 (95% c.i.: 47. 8 -98.4) . in atahualpa, sars-cov-2 rapidly spread across the village, markedly increasing mortality during april and may, 2020 (figure 1) , and infecting 45% of the adult population, in just a few months [6] . during a four-month period, 1.6% of the entire adult population of atahualpa, including 6.9% (27/392) of older adults, died from sars-cov-2related causes. after peaking in april and may, however, mortality significantly decreased. since preventive measures are poorly endorsed by locals, the high proportion of infected individuals and the resulting herd immunity may have contributed to the observed reduction in mortality [9] . atahualpa's mortality scenario is typical of closed populations where inhabitants are immunologically naïve to a rapidly spreading pathogen. to the immunological naivety of these populations, it must be added the adverse circumstances in which they live regarding prediction of the covid-19 spread in african countries and implications for prevention and control: a case study in south africa effective reproductive number estimation for initial stage of covid-19 pandemic in latin american countries covid-19 in latin america: novel transmission dynamics for a global pandemic perspective from ecuador, the second country with more confirmed cases of coronavirus disease 2019 in south america: a review sars-cov-2 in rural latin america. a population-based study in coastal ecuador world health organization. global surveillance for covid-19 caused by human infection with covid-19 virus surveillanceguidance-2020.6-eng.pdf?sequence=1&isallowed=y. accessed on key findings from the atahualpa project: what should we learn? a mathematical model reveals the influence of population heterogeneity on herd immunity to sars-cov-2 indigenous communities in brazil fear pandemic's impact key: cord-254377-j8e8gb0l authors: ali, sadaf; pappachan, joseph m.; mathew, smitha title: acute cor pulmonale from saddle pulmonary embolism in a patient with previous covid-19 – should we prolong prophylactic anticoagulation? date: 2020-06-13 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.039 sha: doc_id: 254377 cord_uid: j8e8gb0l abstract severe corona virus disease 19 (covid-19) is known to be associated with exaggerated risk of thromboembolism. however, the risk associated with mild and moderate illness from covid-19 is unknown, and there is no current recommendation for prophylaxis against thromboembolism in patients after hospital treatment unless there are established thrombophilic risk factors. we report the case of a 52-year old woman, who presented with massive saddle pulmonary embolism after one week of initial hospital discharge, successfully thrombolysed that raises the question of consideration of extended prophylactic anticoagulation even in low risk covid-19 cases. the global pandemic from the corona virus disease 19 (covid-19) caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has affected >6.8 million people with a death toll >4,00,000 while writing this article, across the world affecting almost all countries. although covid-19 has protean clinical manifestations involving almost every organ system in the human body, pneumonia, acute respiratory distress syndrome (ards), diarrhea, septic shock, acute kidney injury (aki), disseminated intravascular coagulation (dic) and rhabdomyolysis are the more commonly described clinical features. 1 arterial and/ or venous thromboembolic events can also be important manifestations of severe cases with covid-19, though the actuarial prevalence or the incidence of this complication is unknown, especially in those with mild disease. a recent autopsy series among 12 cases revealed that unsuspected venous thromboembolism was present in 7 (58%) patients, and pulmonary embolism (pe) was the direct cause of death in 4 (33.3%) patients. 2 acute cor pulmonale and cardiac arrest have also been described in critically ill patients. 3 we report a case of acute massive pe successfully managed by thrombolysis in a patient who was discharged after one week of initial hospital treatment for covid-19 pneumonia which raises serious concerns about the indication for extended prophylactic anticoagulation in such cases. a 52-year-old woman presented with difficulty in breathing and productive cough for 2 weeks with previous history of well-controlled asthma and essential hypertension without any past or family history of thrombophilia. she had bi-basal lung crackles and an oxygen saturation of 93% while breathing 40% oxygen through venturi mask. other initial investigations (and normal laboratory range) were as follows: white cell she was initially managed with intravenous hydration, oral doxycycline, oxygen, and prophylactic enoxaparin. subsequently, she was weaned off oxygen and was discharged 4 days after initial admission. one week later she presented again with a syncopal episode and severe breathlessness, chest tightness, tachycardia, hypoxia, and hypotension. blood profile showed: serum troponin 205 ng/l (5-14), d-dimer 6.26 µg/ml (0-0.5), crp 7 mg/l, and lymphocyte count 0.95 x 10 9 /l. chest radiograph revealed improving bibasilar lung infiltrates in comparison to the radiograph 11 days ago. the electrocardiogram showed s1q3t3 pattern suggestive of probable acute pe. an urgent computed tomographic pulmonary angiogram (ctpa) revealed bilateral extensive thromboembolism in the pulmonary arterial branches ( figure 1a ) and a saddle pe in the main pulmonary artery bifurcation (fig 1b) . there was right ventricular (rv) dilatation and deviation of the interventricular septum to the left ventricle suggesting rv strain pattern (fig 2) . the lung windows of the ctpa showed resolving covid-19 pneumonia ( figure 3a & b) . she was immediately thrombolysed with recombinant tissue plasminogen activator from the intensive treatment unit (itu) with rapid improvement of hypoxia and hypotension. within 16 hours of successful thrombolysis, she was able to maintain oxygen saturations of 98-100% on room air. after the initial management with therapeutic anticoagulation using subcutaneous enoxaparin, she was discharged home on the fourth day of the second hospital admission on oral rivaroxaban 15 mg twice daily for 21 days followed by a maintenance dose of 20 mg daily for 3 more months. based on the observations from multiple clinical studies, severe covid-19 infection requiring itu management is now established as a highly thrombophilic state with an estimated incidence of varying j o u r n a l p r e -p r o o f degrees of thromboembolic episodes ranging from 21-58%. 2-6 a significant chunk of these patients developed thromboembolic events even while on prophylactic anticoagulation therapy challenging our conventional concepts about anticoagulation protocols in the itu management critically ill patients. emerging data and clinical experience suggest an increased prevalence of venous thromboembolic events (vte) in covid-19, especially in patients with severe disease requiring hospitalization, and even among those who are not critically ill. the pathogenesis for covid-19-associated hypercoagulability so far is explained by hypoxia and systemic inflammation secondary to covid-19 that may lead to high levels of inflammatory cytokines and activation of the coagulation pathway. however, the exact mechanisms causing thromboembolic episodes remain elusive. endothelial inflammation with very high levels of von willebrand factor antigen and factor viii, hypoxemia-induced vasoconstriction promoting vaso-occlusion, activation of hypoxia-inducible factors (hifs) that results in induction or inhibition of many genes including tissue factor (tf) and plasminogenactivator inhibitor-1, elevated levels of lupus anticoagulant, direct activation coagulation cascades and endothelial injury by the virus were all proposed as putative mechanisms. 4 all hospitalised patients with covid-19 infection should receive pharmacological thromboprophylaxis as per the standard international recommendations. 7 some groups even recommend empirical therapeutic anticoagulation in severely ill covid-19 cases treated in the itu, based on past experience of very high risk of thromboembolism for these high risk patient groups. 7, 8 fibrinolytic therapy or catheter-based intervention for the removal of thrombus is the treatment of choice for hemodynamically unstable patients with massive pe and acute cor pulmonale. thrombolysis was found to reduce the odds of death (or 0.57; 95% ci 0.37 to 0.87, p = 0.01) and recurrence of pe (or 0.51; 95% ci 0.29 to 0.89, p = 0.02) although increased the risk of bleeding in patients with massive pe. 9 the risk of recurrence after an episode of unprovoked venous thromboembolism treated with anticoagulation for 3 months was found to be 10% within the first year, 16% at two years, 25% at five years, and 36% at 10 years. 10 the u.s. national institute of health (nih) has recently updated the guidelines for antithrombotic therapy in patients with covid-19 who are discharged from the hospital. 12 the guidelines state that routine postdischarge vte prophylaxis is not recommended for patients with covid-19. the benefits of post-discharge prophylaxis for certain high-risk patients without covid-19 led to the food and drug administration approval of two regimens currently: rivaroxaban 10 mg daily for 31 to 39 days, and betrixaban 160 mg on day 1, followed by betrixaban 80 mg once daily for 35 to 42 days. 13, 14 inclusion criteria for the rcts that studied these regimens included: the modified international medical prevention registry on venous thromboembolism (improve)-vte score ≥4 or modified improve-vte score ≥2 and d-dimer level >2 times the upper limit of normal; 13 and age ≥75 years or age >60 years and d-dimer level >2 times the upper limit of normal or age 40 to 60 years, d-dimer level >2 times the upper limit of normal, and previous vte event or cancer. 14 post-discharge vte prophylaxis should consider the individual patient's risk factors, including reduced mobility, bleeding risks, and feasibility before any treatment decision is made. china medical treatment expert group for covid-19. clinical characteristics of coronavirus disease 2019 in china autopsy findings and venous thromboembolism in patients with covid-19: a prospective cohort study acute cor pulmonale in critically ill patients with covid-19 high risk of thrombosis in patients in severe sars-cov-2 infection: a multicenter prospective cohort study venous and arterial thromboembolic complications in covid-19 patients admitted to an academic hospital in confirmation of the high cumulative incidence of thrombotic complications in critically ill icu patients with covid-19: an updated analysis covid-19 and thrombotic or thromboembolic disease: implications for prevention, antithrombotic therapy, and follow-up chinese expert consensus on diagnosis and treatment of coagulation dysfunction in covid-19 thrombolytic therapy for pulmonary embolism marvelous collaborators. long term risk of symptomatic recurrent venous thromboembolism after discontinuation of anticoagulant treatment for first unprovoked venous thromboembolism event: systematic review and meta-analysis ongoing clinical trials on anticoagulation for the patients with covid-19 illness antithrombotic therapy in patients with covid-19 modified improve vte risk score and elevated d-dimer identify a high venous thromboembolism risk in acutely ill medical population for extended thromboprophylaxis extended thromboprophylaxis with betrixaban in acutely ill medical patients key: cord-283590-xvnv17zy authors: chen, dabiao; xu, wenxiong; lei, ziying; huang, zhanlian; liu, jing; gao, zhiliang; peng, liang title: recurrence of positive sars-cov-2 rna in covid-19: a case report date: 2020-03-05 journal: int j infect dis doi: 10.1016/j.ijid.2020.03.003 sha: doc_id: 283590 cord_uid: xvnv17zy the ongoing outbreak of covid-19 that began in wuhan, china, has constituted a public health emergency of international concern, with cases confirmed in multiple countries. currently, patients are the primary source of infection. we report a confirmed case of covid-19 whose oropharyngeal swab test of sars-cov-2 rna turned positive in convalescence. this case highlights the importance of active surveillance of sars-cov-2 rna for infectivity assessment. since december 2019, sars-cov-2 (severe acute respiratory syndrome coronavirus 2; previously known as 2019-ncov) has generated over 70000 cases of covid-19 (corona virus disease 2019, formerly known as novel coronavirus pneumonia, ncp) in china, including 1870 deaths, as of 17 february 2020 (national health commission of the people's republic of china, 2020). the epidemic has been spreading to 25 other countries, with 794 confirmed cases and three deaths, reported by world health organization (who) on 17 february (world health organization, 2020) . respiratory droplets and contact are considered the main routes of transmission. currently, covid-19 patients remain the primary source of infection (chan et al., 2020 ; general office of national health commission and general office of national administration of traditional chinese medicine, 2020; special expert group for control of the epidemic of novel coronavirus pneumonia of the chinese preventive medicine association, 2020). we report a case of covid-19 with recurrently positive sars-cov-2 ribonucleic acid (rna) from an oropharyngeal swab test. a 46-year-old woman developed a fever of 38.3 c with no other apparent symptoms on 17 january 2020. after taking two-day oral antibiotics, the temperature returned normal. on 23 january, she suffered from sore throat, cough, and chest distress, with a body temperature of 37.3 c. the next day, she came to the fever clinic of the third affiliated hospital of sun yat-sen university. she disclosed that she had been traveling in wuhan from 11 to 13 january with a friend who had been diagnosed as a confirmed case of covid-19 on 19 january. she denied any exposure to the huanan seafood market or wild animals. a high-resolution computed tomography (hrct) of the chest was performed immediately, images of which reported multiple patchy ground-glass opacities in bilateral subpleural areas ( figure 1 ). given the travel history and chest hrct findings, she was admitted to an airborne-isolation unit as a suspected case of covid-19. on admission, physical examination revealed normal vital signs with oxygen saturation of 98% while the patient was breathing ambient air. lung auscultation revealed no rhonchi. arterial blood gas analysis indicated no abnormality with arterial oxygen tension (pao2) of 105 mmhg and an oxygenation index of 499 mmhg. blood routine tests, liver function, renal function, myocardial enzymes, electrolyte, and serum procalcitonin were normal. the antigen test for influenza a and b was negative. igm test for influenza a and b, parainfluenza, respiratory syncytial virus, adenovirus, mycoplasma pneumoniae, chlamydia pneumoniae, rickettsia burnetii, and legionella pneumophila was negative. on 24 january, the centers for disease control (cdc) confirmed that the patient's oropharyngeal swab test of sars-cov-2 by qualitative real-time reverse-transcriptase-polymerase-chain-reaction (rt-pcr) assay was positive. according to the diagnostic criteria in china (general office of national health commission and general office of national administration of traditional chinese medicine, 2020), she was confirmed as a covid-19 patient. the patient's respiratory symptoms improved, and she maintained normal body temperature after symptomatic treatment and antimicrobial therapy, including oseltamivir, arbidol, lopinavir/ ritonavir, and moxifloxacin. oropharyngeal swab tests of sars-cov-2 rna were performed repeatedly for surveillance (table 1) . exceptionally, the result was positive on 2 february, with a viral load of 4.56 â 10 2 copies/ml detected by quantitative real-time pcr. the dynamics of chest hrct revealed gradual absorption of lung lesions. on 9 february, she was discharged and encouraged to maintain home quarantine for at least 14 days. sars-cov-2 rna by oropharyngeal swab remained negative in her follow-up visit on 17 february. the who director-general declared that the outbreak of covid-19 constitutes a public health emergency of international concern on 30 january 2020. the spectrum of this disease ranges from mild to life-threatening. some cases might progress rapidly to acute respiratory distress syndrome (ards) and/or multiple organ function failure. an epidemiological survey indicated that the general population is susceptible to sars-cov-2. respiratory droplets and contact are considered the main routes of transmission. covid-19 patients currently remain the primary source of infection. asymptomatic carriers and those in the incubation period may also be infectious ( people with positive sars-cov-2 rna by respiratory tract specimens are probably an infectious source of covid-19. according to the guideline in china, patients should be isolated until two consecutive sars-cov-2 rna tests of respiratory tract specimens are both negative, with an interval of at least 24 h (general office of national health commission and general office of national administration of traditional chinese medicine, 2020). however, the patient we report in this article presented an inconsistent situation. the oropharyngeal swab test for sars-cov-2 rna on 2 february became positive again after two consecutively negative results on 28 january and 30 january, while her respiratory symptoms had already improved, and she had no fever. in other words, she was still capable of transmitting the virus to other people if she had been discharged right after the second negative test. we speculate on the reasons why the results of the sars-cov-2 rna tests, in this case, were fluctuant. first of all, no research has yet accurately established the contagious period of covid-19. besides patients and asymptomatic carriers, those in convalescence may also be infectious. sars-cov-2 rna from respiratory tract specimens may be persistent or recurrently positive during the course of this disease. furthermore, angiotensin-converting enzyme-2 (ace-2), identified as the cell entry receptor of sars-cov-2, was highly expressed in the lungs rather than in the upper respiratory tract (lu et al., 2020; zhou et al., 2020) . the result of the sars-cov-2 rna test likely depends on the viral load of the specimen. therefore, there could be false negatives on occasion for oropharyngeal or nasopharyngeal swabs tests, affected by the site from which the sample was taken, the experience of the operator, and the actual quantity of virus. the bronchoalveolar lavage fluid (balf) specimen test is considered more accurate but with a higher exposure risk. in addition to the above specimens, sars-cov-2 rna can be detected in a patient's sputum, blood, or stool swab by rt-pcr assay. running multiple tests and collecting different specimens would be more effective approaches to maximize sensitivity. combination with the sars-cov-2 rna test and other detective methods such as a specific antigen, igm antibody, or the next-generation sequencing, is also conducive to diagnosis. given the possibility of recurrently positive sars-cov-2 rna in the clinical course and to reduce the risk of transmission in other covid-19 cases, we suggest that: (1) both nasopharyngeal and oropharyngeal swabs test for sars-cov-2 rna should be performed to reduce the false-negative rate. more tests, more specimens, and more methods could be considered. (2) patients in convalescence should also be regularly tested for infectivity assessment, and all the discharged patients should be homequarantined for at least 14 days. this study was supported by grants from the emergency special program for 2019-ncov of sun yat-sen university science and technology project (sysustp-esp) and the emergency special program for 2019-ncov of guangdong province science and technology project (gdstp-esp) (2020b111105001). informed consent was obtained from the patient for publication of this case report and accompanying image. a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster general office of national health commission, general office of national administration of traditional chinese medicine. diagnostic and treatment protocol for novel coronavirus pneumonia (trial version 5, revised form) genomic characterization and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding national health commission of the people's republic of china. an update of novel coronavirus pneumonia outbreak as of 24:00 on transmission of 2019-ncov infection from an asymptomatic contact in germany special expert group for control of the epidemic of novel coronavirus pneumonia of the chinese preventive medicine association. an update on the epidemiological characteristics of novel coronavirus pneumonia (covid-19) novel coronavirus(2019-ncov) situation report -28 a familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period a pneumonia outbreak associated with a new coronavirus of probable bat origin the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-258078-k7y8k1vx authors: jang, sukbin; rhee, ji-young title: three cases of treatment with nafamostat in elderly patients with covid-19 pneumonia who need oxygen therapy date: 2020-05-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.072 sha: doc_id: 258078 cord_uid: k7y8k1vx no effective treatment for covid-19 has been well established yet. nafamostat, known as anticoagulant, has potential anti-inflammatory and anti-viral activities against covid-19. we report three cases of covid-19 pneumonia who progressed while using antiviral drugs and needed supplementary oxygen therapy, improved after treatment with nafamostat. these preliminary findings show the possibility that nafamostat can be considered to be used in elderly patients with covid-19 pneumonia who need oxygen therapy. the effectiveness of nafamostat should be evaluated in further studies. since the covid-19 outbreak started in china, most deaths occur in the elderly or people with underlying diseases. the pathogenesis of covid-19 is still not well understood why the viral infections lead to respiratory failure with a high mortality rate (gao et al., 2020 ). an excessive immune response contributes to covid-19 pathogenesis and lethality (gao et al., 2020 . recently, complement suppression may represent a therapeutic approach to treat covid-19 (gao et al., 2020) . while covid-19 was outbreak in korea, no effective treatment for covid-19 has been well established yet. recently, several journals mentioned the possibility of nafamostat (guo et al., 2020 , hoffmann et al., 2020 , wang et al., 2020 , yamamoto et al., 2016 . nafamostat, serine protease inhibitor, can prevent the fusion of the envelope of the virus with host cell surface membranes, the first step in infection with the causative virus covid-19 by inhibit trpmss2, a human cell surface serine protease (guo et al., 2020 , hoffmann et al., 2020 , yamamoto et al., 2016 . nafamostat inhibits various enzyme systems, such as coagulation and fibrinolytic systems, the kallikrein-kinin system, the complement system, and activation of protease-activated receptors (drugbank, 2020, march 01) . it also inhibits lipopolysaccharide-induced nitric oxide production, apoptosis, and interleukin (il)-6 and il-8 levels in cultured human trophoblasts (drugbank, 2020, march 01) . it is shown to act as an antioxidant in tnf-α-induced ros production (drugbank, 2020, march 01) . therefore, nafamostat is thought to have anti-inflammatory and anti-viral properties to covid-19. three covid-19 patients had the following conditions: pneumonia with progression despite antiviral treatment; were elderly, over 65 years; and had underlying diseases that were known as high risk j o u r n a l p r e -p r o o f factors. these three patients were continuously administered 200mg of nafamostat for 24 hours. this study was approved by the institutional review board of dankook university hospital (dkuh 2020-03-031-001). a 75-year-old man with hypertension and diabetes mellitus was diagnosed with covid-19 on february 26, 2020. he had myalgia, and cough and sputum, which had begun the day before diagnosis. on admission, he was not dyspneic or cyanotic, with a body temperature of 37.0°c, respiratory rate of 20 breaths per minute, heart rate of 75 beats per minute, and blood pressure of 140/90 mmhg. initial laboratory results were as follows: white blood cell (wbc) count 5,150/μl (65% segmented neutrophil), and c-reactive protein (crp) 2.61 mg/dl. initial chest radiography showed infiltrations in both lower lung fields, but high-resolution computed tomography (hrct) on march 2, 2020, revealed multiple, ground-glass opacities located in both lungs. oxygen was supplied beginning march 6 due to desaturation. on march 7, chest radiography showed increased infiltrations, and hrct revealed that the existing lesions had transformed into consolidation. laboratory results on march 8 showed an increased wbc count of 9,510/μl (85% segmented neutrophil) and high crp of 17.79 mg/dl. beginning march 8, he was administered nafamostat. in addition, acetaminophen was administered regularly for fever control. after 2 days of nafamostat administration, his crp level was decreased to 9.13mg/dl and oxygen saturation was maintained above 98% in room air without oxygen supply. his crp level was decreased to 1.32mg/dl, 6 days after administration of nafamostat. on the 11th and 12th days after the nafamostat administration, a negative real-time reverse transcription-pcr (rt-pcr) results for severe acute respiratory syndrome coronavirus 2 was confirmed. a 69-year-old man with hypertension experienced myalgia on february 28, and was confirmed to have covid-19 on march 6, 2020. he had fever from the day of hospitalization, and cough began to develop. physical examination revealed a respiratory rate of 20 breaths per minute, heart rate of 60 per minute, and blood pressure of 150/70 mmhg. initial laboratory results were as follows: wbc count 6,010/μl (74% segmented neutrophil), and crp 0.23 mg/dl. initial chest radiography, showed no infiltrations. however, hrct revealed multifocal consolidations with j o u r n a l p r e -p r o o f peripheral ground glass opacities. respiratory distress occurred on the 9th hospital day and oxygen was supplied. on march 14, chest radiography showed increased infiltrations, and laboratory results on march 15 revealed increased crp of 13.0 mg/dl. beginning march 14, he was administered nafamostat. after 4 days of nafamostat administration, his crp level decreased to 5.27mg/dl and oxygen saturation was maintained above 98% without oxygen supply. we changed the medication to camostat (600 mg/day) 4 days after nafamostat administration. on the 19th and 20th days after the camostat administration, a negative rt-pcr results for severe acute respiratory syndrome coronavirus 2 was confirmed. a 66-year-old man with a history of poliomyelitis and hypertension who had experienced muscle pain since march 2 was diagnosed with covid-19 on march 9, 2020, and was hospitalized on march 15. on admission, he was not dyspneic or cyanotic, with a body temperature of 36.5°c, respiratory rate of 20 breaths per minute, heart rate of 81 per minute, and blood pressure of 132/84 mmhg. initial blood tests revealed that his wbc count was 10,310/μl (75% segmented neutrophil), and crp 3.31 mg/dl. initial chest hrct revealed multiple consolidations with peripheral groundglass opacities located in both lungs. after hospitalization, oxygen therapy was initiated. on march 19, chest radiography showed increased infiltrations, and laboratory results revealed an increased wbc count of 15,210/μl (76% segmented neutrophil). beginning march 19, he was administered 200 mg of nafamostat. after 5 days of nafamostat administration, his wbc count decreased to 7,870/μl (64.1% segmented neutrophil) and oxygen saturation was maintained above 98% in ambient air. a chest x-ray revealed further resolution of both lung infiltrates. he was discharged on day 15 of hospitalization because of improvement in symptoms and a negative rt-pcr test. the patients were all elderly people with underlying disease known as high risk group. at the time of transfer, both clinical and radiological deterioration were observed, and all patients were taking antivirals including lopinavir/ritonavir and hydroxychloroquine. there were no adverse events associated j o u r n a l p r e -p r o o f with nafamosta, and all patients improved and were discharged. according to the previous cases, four other patients with covid-19 pneumonia are currently using nafamostat. nafamostat is a synthetic serine protease inhibitor, which prevents virus fusion and inhibits various enzyme systems to involve in inflammation. recently, emerging evidence shows that covid-19 can be complicated with coagulopathy namely disseminated intravascular coagulation(dic) (kollias a. et al, 2020, april 18) . from the data, it is thought that nafamostat can prevent disease progression by controlling immune system such as the complement cascade, blocking dic, and preventing virus invasion by inhibiting virus fusion on the cell membrane. it was used as a dic dose in patient treatment (0.06~0.2mg/kg/hour) to our patients. we experienced clinical and radiologic improvement in covid-19 patients with pneumonia treated by nafamostat. nafamostat is a relatively safe drug and can be considered to be used in patients with covid-19 pneumonia. in this preliminary uncontrolled cases of 3 elderly patients with exacerbated covid-19 pneumonia, administration of nafamostat was followed by improvement in clinical status. these cases were treated with nafamostat in elderly patients with pneumonia who progressed while using antiviral drugs in a high-risk group with limited sample size and not through a randomized control study, and highly pathogenic coronavirus n protein aggravates lung injury by masp-2-mediated complement over-activation the origin, transmission and clinical therapies on coronavirus disease 2019 (covid-19) outbreak-an update on the status sars-cov-2 cell entry depends on ace2 and tmprss2 and is blocked by a clinically proven protease inhibitor epidemiology, pathogenesis, and control of covid-19 thromboembolic risk and anticoagulant therapy in covid-19 patients: emerging evidence and call for action remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-ncov) in vitro identification of nafamostat as a potent inhibitor of middle east respiratory syndrome coronavirus s protein-mediated membrane fusion using the split-protein-based cell-cell fusion assay key: cord-289304-9srk0ohb authors: bagnato, sergio; boccagni, cristina; marino, giorgio; prestandrea, caterina; d’agostino, tiziana; rubino, francesca title: critical illness myopathy after covid-19 date: 2020-08-05 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.072 sha: doc_id: 289304 cord_uid: 9srk0ohb we describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (icu) due to coronavirus disease 2019 (covid-19). the patient underwent a neurophysiological protocol, including nerve conduction studies, concentric needle electromyography (emg) of the proximal and distal muscles, and direct muscle stimulation (dms). nerve conduction studies showed normal sensory conduction and low-amplitude compound muscle action potentials (cmaps). emg revealed signs of myopathy, which were more pronounced in the lower limbs. the post-dms cmap was absent in the quadriceps and of reduced amplitude in the tibialis anterior muscle. based on these clinical and neurophysiological findings, a diagnosis of critical illness myopathy was made according to the current diagnostic criteria. given the large number of patients with covid-19 who require long icu stays, many of these patients are very likely to develop icu-acquired weakness, as did the patient described here. health systems must plan to provide adequate access to rehabilitative facilities for both pulmonary and motor rehabilitative treatment after covid-19. we describe a patient who developed diffuse and symmetrical muscle weakness after a long stay in the intensive care unit (icu) due to coronavirus disease 2019 . the patient underwent a neurophysiological protocol, including nerve conduction studies, concentric needle electromyography (emg) of the proximal and distal muscles, and direct muscle stimulation (dms). nerve conduction studies showed normal sensory conduction and low-amplitude compound muscle action potentials (cmaps). emg revealed signs of myopathy, which were more pronounced in the lower limbs. the post-dms cmap was absent in the quadriceps and of reduced amplitude in the tibialis anterior muscle. based on these clinical and neurophysiological findings, a diagnosis of critical illness myopathy was made according to the current diagnostic criteria. given the large number of patients with covid-19 who require long icu stays, many of these patients are very likely to develop icu-acquired weakness, as did the patient described here. health systems must plan to provide adequate access to rehabilitative facilities for both pulmonary and motor rehabilitative severe acute respiratory syndrome coronavirus 2 (sars-cov-2) causes coronavirus disease 2019 (covid-19), which reached pandemic-level diffusion in march 2020. patients with covid-19 frequently experience muscular symptoms, such as myalgia, but myopathic changes have not been evaluated fully in this population. a recent review of the neurological complications of included 25 studies with data on skeletal muscle problems, but no study examining the use of electromyography or another diagnostic test to detect myopathic changes (pinzon et al., 2020) . notably, an unexpectedly large number of patients with covid-19 requires intensive care unit (icu) admission and long stays (lewnard et al., 2020) . critically ill patients are likely to develop muscular complications, such as critical illness myopathy (cim), which adversely affect short-and long-term outcomes (vanhorebeek et al., 2020) . in this report, we describe neurophysiological findings from a patient who developed severe muscular weakness, likely due to cim, after hospitalization for covid-19. a 62-year-old woman with a history of hypertension developed fever, cough, myalgia, and diarrhea at the beginning of march 2020. after a few days of treatment with levofloxacin, which resulted in no clinical improvement, she went to the emergency room of a covid hospital in palermo, italy, where sars-cov-2 infection was diagnosed by chest computed tomography (ct) and nasopharyngeal swab testing for sars-cov-2 rna. seven days after clinical onset, the patient was admitted to an infectious disease unit, where she was treated with lopinavir/ritonavir, hydroxychloroquine, and tocilizumab. nine days after onset, the patient's respiratory function worsened, necessitating transfer to an icu, where she underwent endotracheal intubation and mechanical ventilation. the icu stay was complicated by staphylococcus aureus and candida tropicalis bloodstream infections. during her icu stay, the patient received therapy with neuromuscular blocking agents, antibiotics, antifungal drugs, and corticosteroids. after 28 days, she j o u r n a l p r e -p r o o f was moved to an infectious disease unit for 4 days, but respiratory worsening necessitated another transfer to the icu, where she stayed for 2 days. the patient was then moved to a covid pulmonology unit. in the first days of this stay, she presented psychomotor agitation and temporospatial disorientation; a brain ct examination was normal and, after neurological and psychiatric evaluations, the patient was treated with olanzapine for about 3 weeks, which resulted in progressive improvement of her cognitive functions. sixty-eight days post-onset, and with sars-cov-2 negativity on three consecutive nasopharyngeal swab tests, the patient was moved to a rehabilitation unit. at the beginning of rehabilitative treatment, the patient required a 40% fraction of inspired oxygen and presented dyspnea after mild effort. she had muscle atrophy in the lower limbs. segmental muscle strength evaluation showed diffuse and symmetrical muscle weakness, ranging from 3/5 to 4/5 on the medical research council scale for muscle strength assessment, and greater in the lower limbs and proximal muscles. the patient was able to walk a few steps with assistance. deep tendon reflexes were reduced in the lower limbs. the patient's serum creatine kinase level was normal. eighty days post-onset, the patient underwent a thorough neurophysiological protocol, including conventional nerve conduction studies (of the ulnar, peroneal, tibial, and sural nerves), concentric needle electromyography (emg) of the proximal and distal muscles, and direct muscle stimulation (dms). the neurophysiological study was performed bedside using a micromed system plus evolution electromyograph (mogliano veneto, italy). dms was performed in the right quadriceps and tibialis anterior muscles using two monopolar needle electrodes (rich et al., 1997) , and the evoked compound muscle action potential (cmap) was recorded with two monopolar needle electrodes placed about 1.5 cm distal to the midpoint of a line connecting the two stimulating electrodes. the ratio of the amplitudes of the cmaps evoked by motor nerve stimulation and dms was calculated. this ratio aids discrimination between neuropathic and myopathic processes during overall neurophysiological evaluation; values < 0.5 are indicative of neuropathy and those near 1 are indicative of myopathy (rich et al., 1997; trojaborg et al., 2001) . the normal limits were defined as j o u r n a l p r e -p r o o f means ± two standard deviations from normative data from our laboratory (standard age-matched data for the electroneurographic studies; obtained from 14 subjects for the dms study) (bagnato et al., 2011) . the neurophysiological findings are summarized in table 1 stay in the rehabilitation unit lasted 60 days during which the patient received a rehabilitation program 3 hours a day for 6 days a week. at discharge, she did not require oxygen supplementation, had a mild weakness in lower limb proximal muscles and was able to walk without assistance. the patient described here had myopathy, with greater involvement of the proximal muscles in the lower limbs, probably reflecting icu-acquired weakness. indeed, the patient met the clinical and neurophysiological criteria for cim (stevens et al., 2009) . the pathophysiology of cim is complex and not fully understood, but it probably involves microcirculatory changes, metabolic alterations, electrical muscle alterations with abnormal excitation-contraction coupling, and energetic failure with mitochondrial dysfunction (zhou et al., 2014) . a recent metanalysis identified several risk factors associated significantly with icu-acquired weakness (including cim and/or critical illness polyneuropathy) (yang et al., 2018) ; among them, female sex, sepsis, hyperglycemia, use of neuromuscular blocking agents, and lengthy mechanical ventilation and icu stay were present in this case. preventive and supportive measures, such as glycemic control, nutritional intervention, early mobilization, and physical therapy, but no specific therapy, have been shown to be beneficial in cim management [zhou et al. 2014; vanhorebeek et al., 2020] . how covid-19 make patients susceptible j o u r n a l p r e -p r o o f to muscle damage is an open question. in the previous coronavirus outbreak, causing the severe acute respiratory syndrome in 2002-2004, a postmortem study showed a spectrum of myopathic changes, suggesting a common occurrence of cim in non-survived patients (leung et al., 2005) . in conclusion, increasing evidence shows that patients with sars-cov-2 infection may develop various neurological complications as a direct or indirect viral action (pinzon et al., 2020) . in addition, icu-acquired weakness should be suspected and properly diagnosed in all patients who develop symmetrical weakness after hospitalization for covid-19. in light of the large number of patients with covid-19 who require lengthy icu stays, many of these patients are very likely to develop icu-acquired weakness, as did the patient described here, in the next months. since rehabilitation programs can be effective to reverse muscle weakness caused by cim, health systems must plan to provide adequate access to rehabilitative facilities for patients requiring both pulmonary and motor rehabilitative treatment after covid-19. this work received no specific grant from any funding agency in the public, commercial, or not-forprofit sectors. the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. because this report just reviewed clinical data, there was no need of a specific ethical approval. informed consent was signed by the patient for the publication of this report. j o u r n a l p r e -p r o o f ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. neuromuscular involvement in vegetative and minimally conscious states following acute brain injury myopathic changes associated with severe acute respiratory syndrome: a postmortem case series incidence, clinical outcomes, and transmission dynamics of severe coronavirus disease 2019 in california and washington: prospective cohort study neurologic characteristics in coronavirus disease 2019 (covid-19): a systematic review and meta-analysis direct muscle stimulation in acute quadriplegic myopathy a framework for diagnosing and classifying intensive care unit-acquired weakness electrophysiologic studies in critical illness associated weakness: myopathy or neuropathy -a reappraisal van den berghe g. icu-acquired weakness risk factors for intensive care unit-acquired weakness: a systematic review and meta-analysis critical illness polyneuropathy and myopathy: a systematic review key: cord-271495-5906wju4 authors: beldomenico, pablo m. title: do superspreaders generate new superspreaders? a hypothesis to explain the propagation pattern of covid-19 date: 2020-05-11 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.025 sha: doc_id: 271495 cord_uid: 5906wju4 abstract the current global propagation of covid-19 is heterogeneous, with slow transmission continuing in many countries, and exponential propagation in others, in which the time that took to begin this explosive spread varies greatly. it is proposed that this could be explained by cascading superspreading events, in which new infections caused by a superspreader are more likely to be highly infectious. the mechanism suggested for this is related to viral loads. exposure to high viral loads may result in infections of high intensity, which exposes new cases to high viral loads, and so on. this notion is supported by experimental veterinary research. j o u r n a l p r e -p r o o f 3 --the patterns of propagation of the severe acute respiratory syndrome (sars) outbreak of 2003 were not explained by conventional epidemic models that assumed homogeneity of infectiousness. instead, the existing datasets were best matched by models that used negative binomial distributions in which a small proportion of cases were highly infectious (lloyd-smith et al., 2005 , mcdonald et al., 2004 , shen et al., 2003 . data and modelling supported the existence of 'superspreaders' which played a crucial role in propagating the disease by being very efficient at transmitting sars-cov-1, such that in the absence of superspreading events most cases infected few, if any, secondary contacts (stein, 2011) . almost a decade later emerged the middle east respiratory syndrome coronavirus (mers-cov), with analogous infection dynamics involving superspreading events (hui, 2016) . similarly, early modelling and data suggested that a small proportion of cases of covid-19 were responsible for most transmission, which is evidence that superspreaders also play an important role for sars-cov-2 (mackenzie d, 2020, frieden and lee, 2020). explanations of this superspreader status included high viral shedding due to poor immunocompetence, underlying diseases or co-infection, or elevated contact rate due active social behaviour (lloyd-smith et al., 2005 , mcdonald et al., 2004 , shen et al., 2003 , wong et al. 2015 . the propagation of sars-cov-2 has shown to be heterogeneous at a global scale (data publicly shared by the world health organization and johns hopkins university). after the virus started to be reported outside of china, cases were infecting fewer people than expected, compared to the rate of spread in china. by the end of february, over 50 countries outside china had confirmed the infection, but only three of these, south korea, italy and iran, presented notable spread. in south korea, during the first month of viral propagation there were only two to three reports of new infections per day. however, the rapid spread began after one case was linked to 3900 secondary cases in daegu (shim et al., 2020) . in italy, the rapid surge of cases began in a cluster in lombardy after an infected man was hospitalised without precautionary measures and infected other patients (mostly elder people) and health workers. apparently, there was no calm period in iran, where the first two reported cases were fatal, two weeks later there were 1500 cases, and after one month there were over 17000 reported infections. a few weeks later, several other countries underwent a similar exponential growth in the number of cases, despite many of them taking drastic measures to control the epidemic. a notable case was the usa, page 5 of 10 j o u r n a l p r e -p r o o f 4 where the infection was propagating slowly since january 20th until early march, when the daily growth in the number of cases went suddenly from being of one digit to surpassing 30%, remaining above that geometrical growth rate for almost 20 days. this explosive spread began in new york city, where the number of cases reached 20000 in just over two weeks. in contrast, in most countries the infection has been propagating at a slow to moderate pace (e.g. thailand, singapore, egypt, finland, japan, australia, among many others). in general, there have been also contrasts in the apparent case-fatality rate (deaths/reported) depending on the speed of propagation, being much lower in countries with slow spread (e.g. 0.1 % in singapore, 1.4% in australia, 1.8% in thailand) compared with those where the transmission was notably high (e.g. 14% in italy, 12% in spain, 7% in usa). this difference might be too large to be explained solely by detection bias. it appears that within a region sars-cov-2 spreads gradually unless a chain reaction of transmission is triggered. independent superspreading events due to individual variation cannot explain this large-scale heterogeneous pattern of transmission. the occurrence of superspreaders may not be at random and may depend on other superspreaders. it is proposed that infections caused by contact with superspreaders are more likely to result in new superspreaders than those caused by transmission from a less infectious individual. the mechanism by which this would be possible is by exposure to differential viral load. the primary mode of transmission of sars-cov-2 appears to be through exposure to respiratory droplets and direct contact with infected individuals and their contaminated environment (xiao et al., 2017; van doremalen et al., 2020) . droplets may contain a few or a million viral particles, and this differential load determines how much the environment is contaminated and the infective dose a susceptible person is exposed to. a case with a high intensity of infection has the potential of being a superspreader due to high viral shedding. susceptible people exposed to this hypothetical superspreader would be exposed to a high viral dose. infections resulting from exposure to high loads of virus are expected to be of high intensity, as a large quantity of viral particles initiating replication in synchrony might overwhelm the mechanisms of resistance, and the poor control of viral replication may therefore result in a new potential superspreader. this hypothesis has support from veterinary research. for example, in a recent study calves were experimentally infected by bovine viral diarrhoea virus (an j o u r n a l p r e -p r o o f 5 outcome of infection was dose dependent with animals given a higher dose developing severe disease and more pronounced viral replication and shedding. moreover, sentinel calves housed with the lowdose-infected group did not become infected, despite viral shedding being confirmed. other experimental infections also found that viral dose correlated positively with disease severity and viral shedding in other virus-domestic animal systems, such as feline viral rhinotracheitis in cats (gaskell and povey, 2008) , low pathogenic avian influenza virus in chicken (zarkov and bochev, 20) , and equine influenza in ponies (mumford et al., 1990) . under the hypothesis posited here, cases with low-to-moderate intensity of infection would mainly yield new infections of low-to-moderate severity and viral shedding in people who are not in risk groups. replication, generating a 'domino effect'. the severity of the disease caused by high viral loads is expected to be high. this would be due to extensive cell damage caused by large amounts of virus and also due to the resulting immune response. the virulence arising from an infection by sars-cov-2 is related to inflammatory self-damage (quin et al., 2020) , and it is expected that an infection initiated by a large number of viral particles would generate a stronger immune response, compared to infections caused by a low viral dose. therefore, a case resulting from an exposure to high viral loads has the potential to develop severe disease and also of being highly infectious. it was found that in mers patients the severity of the disease was positively correlated with viral load (min et al., 2016) , and the same was recently reported for covid-19 2020; zou et al., 2020) . it could be argued that individuals with higher viral loads are more likely to be hospitalised or die, and therefore would be less likely to contribute to community transmission as superspreaders. however, it should be taken into account that the outcome of an exposure to a high viral dose will largely depend on the tolerance (ability to reduce the damage of an infection) of an individual (råberg et al., 2009) . given equal resistance (ability to limit the infection), exposure to high viral loads will result in severe disease in the less tolerant and high infection intensity with few manifestations in the more tolerant. the latter case is of special concern, because in these individuals the clinical signs would be mild or absent, and therefore are likely to be undetected, exposing many people to high viral loads. on the other hand, severe cases may be important sources of disease in hospitals . for example, in j o u r n a l p r e -p r o o f 6 argentina, 17% of the cases reported to date are healthcare workers (infobae, 2020) . therefore, the presence of superspreaders in hospitals could make them nodes where cascades of superspreading events emerge, which is consistent with what was observed in lombardy. disease is traditionally studied as a binary outcome, infected or non-infected. the concepts presented here alert us to the value of studying disease as a continuous variable (i.e. infection intensity) (beldomenico and begon, 2010) . measuring the intensity of an infection is crucial because it may be related to the virulence as well as the infectiousness. there are many studies of different viral diseases in which the length of viral shedding is recorded, yet very few produced data on the viral shedding load. the hypothesis posited here needs to be tested by empirical and theoretical studies, but this requires that data on viral load (viraemia and shedding) are urgently collected. if superspreaders generate new superspreaders by exposing susceptible people to large viral loads, this mechanism should be immediately acknowledged and considered in the responses being undertaken. in particular, emphasis should be placed on the isolation or strict distancing of people of risk groups, as they would not only have more chances of developing a more severe disease (with the potential of overwhelming the health system), but they could also be source of high viral loads. in addition, aggressive contact tracing and testing would allow quick identification of tolerant superspreaders, who might be key elements of propagation. are sars superspreaders cloud adults? disease spread, susceptibility and infection intensity: vicious circles? identifying and interrupting superspreading events-implications for control of severe acute respiratory syndrome coronavirus 2. emerg infect dis the dose response of cats to experimental infection with feline viral rhinotracheitis virus super-spreading events of mers-cov infection coronavirus in argentina: 9 deaths among healthcare workers and the number of infected is still rising viral dynamics in mild and severe cases of covid-19 superspreading and the effect of individual variation on disease emergence sars in healthcare facilities comparative and kinetic analysis of viral shedding and immunological responses in mers patients representing a broad spectrum of disease severity experimental infection of ponies with equine influenza (h3n8) viruses by intranasal inoculation or exposure to aerosols dysregulation of immune response in patients with coronavirus 2019 (covid-19) in wuhan, china decomposing health: tolerance and resistance to parasites in animals superspreading sars events transmission potential and severity of covid-19 in south korea superspreaders in infectious diseases viral dose and immunosuppression modulate the progression of acute bvdv-1 infection in calves: evidence of long term persistence after intra-nasal infection aerosol and surface stability of sars-cov-2 as compared with sars-cov-1 exploring the reasons for healthcare workers infected with novel coronavirus disease 2019 (covid-19) in china the role of super-spreaders in infectious disease role of fomites in sars transmission during the largest hospital outbreak in hong kong influence of inoculation dose of avian h6n2 influenza a virus on virus shedding and humoral immune response of chickens after artificial experimental intravenous infection key: cord-297715-qcwp2jdv authors: machida, masaki; nakamura, itaru; saito, reiko; nakaya, tomoki; hanibuchi, tomoya; takamiya, tomoko; odagiri, yuko; fukushima, noritoshi; kikuchi, hiroyuki; amagasa, shiho; kojima, takako; watanabe, hidehiro; inoue, shigeru title: changes in implementation of personal protective measures by ordinary japanese citizens: a longitudinal study from the early phase to the community transmission phase of the covid-19 outbreak date: 2020-05-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.039 sha: doc_id: 297715 cord_uid: qcwp2jdv objectives: to clarify changes in the implementation of personal protective measures among ordinary japanese citizens from the early phase of the covid-19 outbreak to the community transmission phase. methods: this longitudinal, internet-based survey included 2,141 people (50.8% men; 20-79 years). the baseline and follow-up surveys were conducted from february 25-27, 2020 and april 1-6, 2020, respectively. participants were asked how often they implemented the 5 personal protective measures recommended by the world health organization (hand hygiene, social distancing, avoiding touching the eyes, nose and mouth, respiratory etiquette, and self-isolation) in the baseline and follow-up surveys. results: the prevalence of 3 of the 5 personal protective measures significantly improved in the community transmission phase compared to the early phase. social distancing measures showed significant improvement, from 67.4% to 82.2%. however, the prevalence of avoiding touching the eyes, nose and mouth, which had the lowest prevalence in the early phase, showed no significant improvement (approximately 60%). multivariate logistic regression analysis revealed, men and persons of low-income households made fewer improvements than women and persons of high-income households. conclusions: the prevalence of personal protective measures by ordinary citizens is improving, however there is potential for improvement, especially in regard to avoiding touching eyes, nose and mouth. with no end in sight to the rapidly evolving coronavirus disease pandemic, a critical element in reducing transmission of the virus is rapid and widespread behavior change in ordinary citizens (betsch et al., 2020) . many governments and health authorities have called on ordinary citizens to implement personal protective measures, such as hand hygiene, respiratory etiquette, and social distancing measures, since the early phase of the covid-19 outbreak (jmhlw, 2020a, u.s.cdc, 2020, who, 2020a). we recently reported the results of a survey on the implementation status of personal protective measures by ordinary citizens conducted on february 25, 2020 during the early phase of in japan (machida et al., 2020) . in that study, we found that in the early phase of covid-19 there was j o u r n a l p r e -p r o o f low prevalence among ordinary japanese citizens in the implementation of social distancing measures and avoiding touching the eyes, nose and mouth, 2 of the 5 personal protective measures recommended by the world health organization (who) (who, 2020a the company, then invited the 2,400 respondents of the baseline survey to participate in a follow-up survey by email on april 1, 2020. on that day, the number of reported covid-19 cases in japan was 2,178, and the number of patients had increased rapidly, mainly in tokyo (who, 2020b). the questionnaires were placed in a secure section of a website, and potential respondents received a specific url in their invitation email. the 2,400 respondents to the baseline survey responded to the questionnaire voluntarily, and the response cut-off date was april 6. on april 7, a day after the completion date of the survey, the japanese government declared a state of emergency (prime minister of japan, 2020). reward points valued at 50 yen were provided as an incentive for participation (approximately 0.5 us dollars, as of april 2020) in both the baseline and follow-up survey. participants described their self-reported implementation of the 5 personal protective measures (hand hygiene, social distancing measures, avoiding touching the eyes, nose and mouth, respiratory etiquette, and self-isolation) recommended by the who (who, 2020a). regarding the 4 personal protective j o u r n a l p r e -p r o o f measures, other than self-isolation, participants were asked about the frequency of implementation during the previous week and responded using a 4-point-likert scale (1: "always", 2: "sometimes", 3: "rarely", or 4: "never"). as for social distancing measures, participants were asked to disclose the frequency in which they avoided places where many people would be gathered together. regarding self-isolation, the participants were asked the question, "if you have a fever or a cold, can you take time off from work?" participants responded using a 5-point likert scale (1: "definitely can", 2: "probably can", 3: "probably can't", 4: "definitely can't" or 5: "not working". participants answered the same questions in both the baseline survey and the follow-up survey. in the baseline survey, participants gave information about their sex, age, marital status (not married/married), working status (working/not working), smoking status (smokers/non-smokers), past medical history (hypertension, diabetes, and respiratory disease), and residential area (tokyo/other). in the follow-up survey, participants were also asked about their living arrangement (with others/alone). in addition, the research company provided categorized data as follows: educational attainment (university graduate or above/below), and household income level (< 5 million yen or ≥ 5 million yen). regarding the 5 personal protective measures, when a participant responded with 1 ("always"/"definitely can") or 2 ("sometimes"/"probably can") on the 4-point-likert scale, it was determined that the personal protective measures had been implemented. in both the baseline survey and follow-up survey, we clarified the prevalence of each personal protective measure, and the implementation of all personal protective measures. in regard to self-isolation and implementing all personal protective measures, those who selected 5 ("not working") in the baseline survey or followup survey, were excluded from the analysis (n=776). the mcnemar test was performed to compare the prevalence of each personal protective measure between the baseline survey and follow-up survey. to clarify the association between each sociodemographic factor and behavior changes related to each personal protective measure, a multivariate logistic regression analysis was performed to focus on those who did not implement the personal protective measure in the baseline survey. the dependent variable was set as a dichotomous variable coded as "1" if the personal protective measure was adopted in the follow-up survey and "zero" otherwise. the dependent variable was prepared for each of the 5 smoking status (smokers/non-smokers), residential area (tokyo/other), educational attainment (university graduate or above/below), and household income level (< 5 million yen or ≥ 5 million yen). regarding self-isolation, those who selected 5 ("not working"), in either the baseline survey or followup survey, were excluded from the analysis, therefore working status was removed from the aforementioned independent variables. statistical analyses were performed using ibm spss statistics for windows, version 26 (ibm japan, tokyo, japan). two-sided p values less than 0.05 were considered to be statistically significant. of the 2,400 respondents in the baseline survey, valid responses were obtained from 2,141 respondents in the follow-up survey (response rate: 89.2%, table 1 ). we set out to determine the status of behavior change in personal protective measures among ordinary japanese citizens from the early phase of the covid-19 outbreak to the community transmission phase, in addition to the association between each sociodemographic factor and behavior change. there were significant improvements in social distancing measures during the community transmission phase compared to the early phase of the covid-19 outbreak. however, the prevalence of avoiding touching the eyes, nose and mouth was approximately 60%, indicating no significant improvement. moreover, men and persons with low household income levels made fewer behavior awareness activities related to avoiding touching the eyes, nose and mouth, which is assumed to be the reason for the lack of improvement in that behavior. moreover, face touching behavior is a common habit (kwok et al., 2015) , therefore unless one is extremely careful, it may be difficult to stop. this study suggests that the implementation status of personal protective measures in ordinary citizens can change with each pandemic phase and awareness activities that are introduced. it may be important to monitor these changes for developing effective educational activities. the multivariate logistic regression analysis revealed that men and persons with low household income levels made fewer behavior changes adopting personal protective measures. it may be effective to focus on populations with such sociodemographic characteristics when providing education on personal protective measures during an infectious disease pandemic, which can lead to constraints on both time and resources. previous studies on self-isolation have reported that people who are unable j o u r n a l p r e -p r o o f to work from home or lose income when absent from work have a lower rate of self-isolation (blake et al., 2010 , eastwood et al., 2009 . it may be essential to implement recommendations for working from home as well as salary compensation to enhance the prevalence of self-isolation, rather than simply executing awareness activities. this study has some limitations that should be considered. the most important point is the fact that participants in this study were recruited from people enrolled at a single internet research company, and the results may have been affected by a selection bias. relatively little is known about the characteristics of people in online communities (wright, 2017) . furthermore, the age and sex demographics of the participants in this study were different from that of the general japanese population (statistics bureau of japan, 2019). second, the results may only be directly applied to the japanese population. in the case of other populations with different cultural, ethnic, and geographical backgrounds, the prevalence of personal protective measures and implementation status of behavior change may be differ considerably when compared with those reported in the present survey. despite these limitations, to the best of our knowledge, this study is the first study to clarify the behavior changes in personal protective measures among ordinary japanese citizens from the early phase of covid-19 in japan to the community transmission phase, and to identify an association between the behavior changes and each sociodemographic factor. j o u r n a l p r e -p r o o f citizens from the early epidemic phase of covid-19 to the community transmission phase. the prevalence of many personal protective measures, including social distancing measures, by ordinary citizens during the covid-19 pandemic improved, but leaves potential for improvement, especially in terms of avoiding touching eyes, nose and mouth. monitoring these changes may be relevant when considering effective educational activities to raise and promote awareness and adherence to preventive measures. this research did not receive any specific grants from funding agencies in the public, commercial, or not-for-profit sectors. this study was approved by the ethics committee of tokyo medical university, tokyo, japan (no: t2019-0234). informed consent was obtained from all the respondents. the authors declare no conflicts of interest. j o u r n a l p r e -p r o o f monitoring behavioural insights related to covid-19 employment and compliance with pandemic influenza mitigation recommendations knowledge about pandemic influenza and compliance with containment measures among australians about coronavirus disease expert meeting on the novel coronavirus disease control analysis of the response to the novel coronavirus (covid-19) and recommendations (exerpt) preventing outbreaks of the novel coronavirus face touching: a frequent habit that has implications for hand hygiene adoption of personal protective measures by ordinary citizens during the covid-19 outbreak in japan declaration of a state of emergency in response to the novel coronavirus disease joint message from the governors of tokyo and four neighboring prefectures cdc). how to protect yourself basic protective measures against the new coronavirus world health organization (who), coronavirus disease (covid-2019) situation reports researching internet-based populations: advantages and disadvantages of online survey research, online questionnaire authoring software packages, and web survey services sometimes", or "definitely can", or "probably can" (in the case of self-isolation) for each personal preventive measure at the time of the baseline survey, and "implementing each measure" at the time of the follow-up survey. participants who had already implemented a personal protective measure at the time of the baseline survey were excluded in the analysis for that particular protective measure. independent variables were sex, age (older adults ≥ 65 years old/persons under 65 years old), marital status (not married/married), working status (working/not working), living arrangement (with others/alone), smoking status (smokers/nonsmokers), residential area (tokyo/other), educational attainment if you have a fever or cold, can you take time off from work?" participants selected one of the items of the 5 point-likert scale. those who selected 5 the authors declare that they are unaware of any competing financial interests or personal relationships that could have influenced the work reported in this paper. we would like to express our sincere gratitude to all the participants who enrolled in this study. key: cord-291638-oatrjbo3 authors: kang, dayun; choi, hyunho; kim, jong-hun; choi, jungsoon title: spatial epidemic dynamics of the covid-19 outbreak in china date: 2020-04-03 journal: int j infect dis doi: 10.1016/j.ijid.2020.03.076 sha: doc_id: 291638 cord_uid: oatrjbo3 background: on 31 december 2019 an outbreak of covid-19 in wuhan, china, was reported. the outbreak spread rapidly to other chinese cities and multiple countries. this study described the spatio-temporal pattern and measured the spatial association of the early stages of the covid-19 epidemic in mainland china from 16 january–06 february 2020. methods: this study explored the spatial epidemic dynamics of covid-19 in mainland china. moran’s i spatial statistic with various definitions of neighbours was used to conduct a test to determine whether a spatial association of the covid-19 infections existed. results: the spatial spread of the covid-19 pandemic in china was observed. the results showed that most of the models, except medical-care-based connection models, indicated a significant spatial association of covid-19 infections from around 22 january 2020. conclusions: spatial analysis is of great help in understanding the spread of infectious diseases, and spatial association was the key to the spatial spread during the early stages of the covid-19 pandemic in mainland china. on 31 december 2019 the chinese government first reported an outbreak of coronavirus disease in wuhan, the capital of hubei province in china. the outbreak rapidly spread from wuhan into all provinces of china and at least 24 countries. as of 06 february 2020 31,481 cases of covid-19 were officially confirmed in mainland china, including 639 deaths. a total of 22,112 cases were confirmed in hubei province, accounting for 70.89% of the total cases. until now, studies evaluating the spatial spread of the covid-19 pandemic in china are limited. however, understanding the spatial spread of the covid-19 outbreak is critical to predicting local outbreaks and developing public health policies during the early stages of covid-19. previous studies have described the spatial spread of severe acute respiratory syndrome (sars) in beijing and mainland china (meng et al., 2005; fang et al., 2009) . one study also considered the different types of connections between cities to calculate the spatial association (meng et al., 2005) . other studies have analyzed the epidemic data of the middle east respiratory syndrome coronavirus (mers-cov) in saudi arabia using various spatial approaches (adegboye et al., 2017; lin et al., 2018; al-ahmadi et al., 2019) . this study investigated the spatial epidemic dynamics of the covid-19 outbreak in mainland china. it also measured and compared the spatial association of the daily epidemic data. different spatial connection assumptions between the provinces regarding possible pathways for the spread of covid-19 (meng et al., 2005) were considered. the objective was to provide spatial dynamic information about the spread of covid-19 for infection prevention and control. the covid-19 dataset was obtained from a chinese website that provides real-time information on outbreaks of epidemic diseases (https://ncov.dxy.cn/ncovh5/view/pneumonia). the website updates data on newly confirmed cases in mainland china by province and date. there are 31 provinces in mainland china, and this study used 3 weeks' data from 16 january to 06 february 2020, which was during the early stages of covid-19 in china. data before 16 january 2020, the very early stage of covid-19, was not examined because of data reliability concerns. other datasetssuch as population, population density, number of licensed doctors, and hospital and health centre beds per 1000 inhabitants by provincewere acquired from a website (statista, 2020). all population-related and medical resource datasets were collected in 2018; these were the most recent data that could be obtained. figure 1 shows a map of cumulative cases by province. the number of cumulative cases is the sum of the newly confirmed cases from 16 january-06 february 2020. the largest number of cases was in hubei province, of which wuhan is the capital city. figure 2 presents the population and population density (populaiton/km 2 ) for each province in 2018. guangdong and shanghai had the highest population and population density, respectively. hubei ranked ninth in population and thirteenth in population density. as shown in figure 3 , shandong has the highest number of doctors and hospital beds (per 1000 inhabitants), whereas hubei ranks ninth and seventh for the number of doctors and hospital beds, respectively. table 1 shows detailed information for each province. to show the spatial association of covid-19, moran's i statistic was used for each day with various types of neighbourhoods (li and calder, 2007) . moran's i statistic measures the spatial autocorrelation and is calculated as follows: where i and j were the region indexes and w ij indicated the adjacency between area i and area j. this study considered different types of adjacency. y i and y j denoted the number of newly confirmed cases in areas i and j, respectively, and y was the average of the number of newly confirmed cases in the entire region. a value of 0 indicated that there was no spatial autocorrelation in the data. a positive moran's i value indicated the clustering of similar values, whereas a negative moran's i value indicated the clustering of dissimilar values. the larger the absolute moran's i value, the stronger the spatial autocorrelation. the number of cases in this study was skewed, so the spatial dependency may not have been properly captured. therefore, to adjust for the skewness, logarithmic transformation of the newly confirmed cases was used instead of the number of cases itself. because there were many 0 in the dataset, 0.01 was added to the data for log transformation. similar to that in a previous study (meng et al., 2005) , six different types of neighbourhoods were used. in model 1, two provinces were considered adjacent if they shared a border. in model 2, the distance between two provinces was used. in this case, the centroid for each province was determined using the gcentroid function in the rgeos package of statistical software r (bivand et al., 2019) . thined as the euclidean distance between the centroids of these provinces. the extent to which the two provinces were adjacent was defined as the inverse of the distance. in models 1 and 2, spatial adjacency was defined by geographical information, which is the usual method for examining spatial relationships. as covid-19 is spread from person to person, population and population density were the key foci. thus, models 3 and 4 considered population and population density. the population (population density) for each province was ranked. a province was defined as adjacent to both the previous and following ranked provinces. thus, the first-ranked and last-ranked provinces only had one adjacent neighbour. in terms of medical care resources, models 5 and 6 considered the number of doctors and hospitals or medical centre beds. the definition of an adjacent neighbour was the same as that in models 3 and 4. moran's i function was used in the ape package of the statistical software r (paradis et al., 2019) . the significance level of moran's i test was 0.05. figure 4 shows the time series plot of the newly confirmed cases for each day. the number of cases for each day was the sum of all cases in mainland china. as shown in figure 4 , the number of cases increased almost exponentially. to prevent an exponential spread over mainland china, it was important to detect the spatial spread in the early stages. because covid-19 spread from hubei province, the epicentre of the outbreak, the number of newly confirmed cases in the provinces neighbouring hubei was investigated. the provinces of hunan, sichuan and tianjin were selected as representative areas of firstorder, second-order and third-order neighbouring provinces, respectively. the daily number of confirmed cases in hubei is shown in the upper panel of figure 5 . the lower panel of figure 5 shows the daily number of confirmed cases in hunan, sichuan and tianjin. from 22 january the number of newly confirmed cases in hunan clearly increased. the infection first increased in hubei and then in the first-order neighbouring provinces such as hunan, and the second-order neighbouring provinces such as sichuan. the infection finally spread to the third-order neighbouring provinces, including tianjin. this supports the fact that covid-19 spread spatially and that investigation of spatial dependency is very essential. this study examined whether a spatial association existed in the cases of covid-19 in china. it used moran's i statistic, a measure of spatial association, for the number of confirmed cases with different types of neighbourhoods. figure 6 shows moran's i statistic and its p-value for each day in models 1-6. overall, the p-values in figure 6 are very close to a value of 0 in models 1-5, except for the first few days. on 22 january models 1-4 first detected a significant spatial dependency on the number of newly confirmed cases. since approximately 24 january, the number of newly confirmed cases show significant spatial dependency in models 1 and 2. the maximum value of moran's i statistic in models 1 and 2 is 0.4598 and 0.0841, respectively. the further the statistic is from 0, the stronger the spatial dependency. therefore, the numbers 0.4598 and 0.0841 are significant, with p-values < 0.05. for population-related neighbourhoods, both models 3 and 4 show a spatial clustering tendency since 22 january, except for 2 and 4 days, respectively. among the days with significant spatial dependency, the maximum value is 0.6991 and 0.7336 in models 3 and 4, respectively. models 3 and 4 also have significant p-values < 0.05. for medical-care-based neighbourhoods, model 5 shows a spatial association since 23 january except 2 days. however, no spatial association exists in model 6. since 23 january, the averagep-value is 0.0129 and 0.6638in models 5 and 6, respectively, which show a significant difference. this study is the first to provide information on the spatial and temporal patterns of the covid-19 pandemic in mainland china. in the early stage of the covid-19 outbreak, new cases occurred intensively in the hubei province. over time, the cases spread to provinces neighbouring hubei; the first-order neighbouring provinces showed a particularly increased number of confirmed cases after 22 january. then, the second-order and third-order provinces showed a steeply increasing number of cases from 23 january and 24 january, respectively. this shows the spread of covid-19. eventually, the impact spread to all provinces in mainland china. this study investigated the spatial dependency through moran's i with different types of spatial connections. except for the medical centre bed-based neighbourhood, a spatial clustering tendency was observed in every neighbourhood type from approximately 22 january. the regions connected by express trains to wuhansuch as shenzhen, shanghai and beijinghad five, two and two confirmed cases, respectively on 21 january, the early stage of covid-19 in china. this implies the possibility that covid-19 had spread from wuhan to other areas via the transportation (zhao et al., 2020) . this possibility also supports the spatial dependency we detected in this study. on 23 january, the chinese government closed off wuhan city to prevent the spread of covid-19. these findings could link with such a government policy. the results of the evaluation using geographical and distance-based neighbourhoods showed that covid-19 is highly likely to spread between geographically adjacent regions. this may be because people in adjacent regions tend to interact with each other. in addition, moran's i using population-based neighbourhoods also showed a strong spatial association. more people are likely to be infected with the virus in densely populated regions, which leads to the active spread of covid-19 to other areas. finally, having many doctors in a region indicates that the region can accommodate many severely ill patients, which can lead to the spread of the virus. this result is consistent with that of a previous study (meng et al., 2005) . in addition, this study conducted the same spatial analysis using the ranks of the newly confirmed cases in a nonparametric approach because the data are quite skewed. the results were almost the same, except that there was a spatial association for a few more days. covid-19 has been affecting countries worldwide, and the world health organization has declared the covid-19 outbreak a public health emergency of international concern. this study demonstrated that in the early stages of the covid-19 pandemic, the disease dramatically spread from region to region in mainland china. examining the spatial spread in the early stages is very important to prevent further transmission. it is believed that this study is the first to investigate the virus's spatial spread to various types of neighbourhoods in mainland china. although this study was conducted in the early stages of the covid-19 outbreak to determine whether there was a spatial association, it did have a few limitations. first, it used the reported dataset for the daily number of newly confirmed cases in the 31 provinces of china. this did not include the number of suspected cases, so it was difficult to understand the spatio-temporal transmission of covid-19. however, it was important to investigate the spatial and temporal characteristics of the covid-19 outbreak at an early stage. second, it considered six types of neighbourhoods; other types of neighbourhoods were not covered in this study, such as the urban-rural relationship, which might have also been significant (meng et al., 2005) . third, it only investigated spatial spread in mainland china. as infections have also occurred in other countries, investigating the global spatial spread of covid-19 might be important to manage covid-19. future research, such as a study examining the spatial tendencies of the deaths and recoveries from covid-19, will contribute to the control and prevention of this disease. through such work, it will be able to be determined which factors affect death and recovery. ethics approval and consent to participate:no human or animal samples were included in the research presented in this article; therefore, ethical approval was not necessary. availability of data and materials:the datasets used and analysed during the current study are available from the websites https://ncov.dxy.cn/ncovh5/view/pneumonia and http://statista. com. spatial modelling of contribution of individual level risk factors for mortality from middle east respiratory syndrome coronavirus in the arabian peninsula spatiotemporal clustering of middle east respiratory syndrome coronavirus (mers-cov) incidence in saudi arabia interface to geometry engine geographical spread of sars in mainland china beyond moran's i: testing for spatial dependence based on the spatial autoregressive model modeling the spread of middle east respiratory syndrome coronavirus in saudi arabia understanding the spatial diffusion process of severe acute respiratory syndrome in beijing analyses of phylogenetics and evolution the association between domestic train transportation and novel coronavirus (2019-ncov) outbreak in china from 2019 to 2020: a data-driven correlational report competing interests: the authors declare no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.funding: this work was supported by the research fund of the basic science research program through the national research foundation of korea (nrf) funded by the ministry of education (nrf-2018r1d1a1b07047712) and by the government-wide r&d fund project for infectious disease research (gfid), republic of korea (grant number: hg18c0088).authors' contributions: j.c. designed the study; d.k. and h.c. contributed to data acquisition; d.k., h.c. and j.c. carried out the statistical analysis; d.k., h.c., j.h.k., and j.c. drafted the manuscript. all authors contributed to the interpretation of data and revision of the manuscript. all authors read and approved the final manuscript. we thank all of the people who were struggling in the healthcare fields to overcome the covid-19 outbreak. this study was performed under the research project named 'research and development on integrated surveillance system for early warning of infectious diseases (risewids).' key: cord-008219-ng9xb46c authors: lassmann, britta; madoff, lawrence c. title: highlights from the 6(th) international meeting on emerging diseases and surveillance (imed 2016) vienna, austria from nov 3 to 7, 2016 date: 2016-12-09 journal: int j infect dis doi: 10.1016/j.ijid.2016.12.008 sha: doc_id: 8219 cord_uid: ng9xb46c nan [ 6 _ t d $ d i f f ] the century of epidemics imed 2016 speakers from all regions of the world agreed that over the course of the coming century, epidemics are likely to occur more frequently, as will the risk of global pandemics. the world's increasing population, higher demand for protein, climate change, increasing mobility, social vulnerability and political instability were only a few of the factors discussed that contribute to the projected increase. at the same time, rapid advances in science and improvements in technology and data sharing offer new ways to prevent, detect, predict and respond to those threats. although we are not able to prepare when, where or which pathogen will emerge next, we will be better prepared to prevent the next pandemic. the general public's interest in emerging infectious diseases was highlighted in a poster presentation by dr. [ 1 7 _ t d $ d i f f ] daniel lucey and colleagues, who showed details of a planned exhibit on ''exploring pandemics: a smithsonian museum endeavor for the public'' at the smithsonian national museum of natural history in washington, dc. the exhibit is scheduled to open in early 2018 through early 2020, coinciding with the 100-year commemoration of the 1918-1920 influenza pandemic and will offer the public an opportunity to explore and understand better 10 epidemics caused by zoonotic viruses from around the world. [ 7 _ t d $ d i f f ] one world -one health: transboundary emerging diseases in humans, animals and wildlife imed opened with a plenary session dedicated to transboundary emerging diseases in an increasingly interconnected world. professor albert osterhaus talked about hiv, avian flu, sars, mers-cov, ebola and zika as some of the diseases that originated in animals and passed to humans. while many of these have been well studied, there remain significant gaps in understanding the linkages of infection, making it challenging to predict and prepare for the next epidemic. several speakers presented results on studies that further examined zoonotic disease spread and aimed at identifying pathogens and environments most conducive to spillover to humans. professor christine kreuder johnson and professor rudovick kazwala discussed results from usaid's emerging pandemic threats predict project, that uses a riskbased strategy to investigate emerging diseases threats. dr. kreuder johnson's team examined common animal hosts and convergent mechanisms involved in past spillovers of zoonotic viruses in order to identify high-risk interfaces for surveillance activities and interventions aimed at prevention. the team found that viruses transmitted to humans had significantly higher host plasticity. in other words, they were reported in a more taxonomically diverse host range. viruses with higher host plasticity were also more likely to amplify viral spillover by secondary human-to-human transmission and have broader geographic spread. dr. kazwala reported on results from the predict project in tanzania where bats, rodents and non-human primates were subjected to molecular virology diagnostic tests and revealed the presence of 64 viruses including 48 novel viruses. international journal of infectious diseases 53s (2016) 1-3 international journal of infectious diseases j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / i j i d during the oral abstract presentation session on one health -diseases across species boundaries, toph allen from ecohealth alliance and colleagues shared results from an updated model assessing the global distribution of zoonotic emerging infectious disease risk. highest risk of emergence was concentrated in tropical regions where wildlife biodiversity is high, human populations dense and growing, and land use change is occurring rapidly. these regions were thought most likely to produce the next emerging infectious disease event, and therefore most valuable for surveillance in wildlife, livestock or people. dr. [ 1 8 _ t d $ d i f f ] ireen shanta and colleagues from the international centre for diarrheal disease research in bangladesh reported data from a cross sectional survey of 9,512 households to identify hotspots of human exposure to rodents, bats and monkeys in bangladesh. they concluded that more than 13.6 million people in bangladesh are exposed to rodents each month, more than 800,000 to bats and more than 80,000 to monkeys putting them at risk for contacts to pathogens from those species. to identify early signals for the emergence, spill over and spread of animal pathogens, dr. julio pinto (food and agricultural organization of the un) then called for a new mindset in the way the international community coordinates and manages disease emergence. the new approach should be multi-disciplinary and should strengthen local capacities in epidemiological analysis, use open analytical tools and gis platforms, integrate new technologies such as mobile devices and rapid diagnostics and be committed to the open sharing of data. since the last imed, flaviviruses have emerged as prominent threats in the world. the flavivirus session addressed the ongoing zika virus epidemic in the americas and other regions of the world and the yellow fever virus outbreak in africa, which threatened to go global. a major concern of the zika virus epidemic is the association of maternal infection with birth defects, a complication that has not been seen with flavivirus infections in humans in the past but has been seen with congenital infections in animals. professor james maclachlan discussed what is known about congenital infections of animals with flaviviruses and highlighted the critical role of the timing of infection. for example, infections with bluetongue virus (btv) have clearly shown the critical role of gestational age in determining outcome. fetuses infected prior to mid-gestation that survive congenital btv infection are born with cavitating central nervous system defects that range from severe hydranencephaly to cerebral cysts (porencephaly). bunyaviruses cause gestational age-dependent teratogenesis in fetal ruminants but, in addition to cavitating central nervous system defects, affected fetuses are born with contracted limbs -congenital hydranencephaly/arthrogryposis syndrome. dr. vanessa van der linden, a pediatric neurologist from recife, in northeastern brazil then gave a heartbreaking description of zika[ 1 9 _ t d $ d i f f ] -related neurologic complications. recife is one of the areas hardest hit by the zika epidemic and dr. van der linden was one of the first to recognize the microcephaly epidemic in this area. she reported patients suffering from the full range of manifestations including craniofacial disproportion, spasticity, seizures, irritability, brainstem dysfunction, limb contractures including arthrogryposis, hearing and ocular abnormalities, and brain anomalies detected by neuroimaging. she emphasized the importance of vigilant health professionals to recognize changes in the neurodevelopment during the first years of life and the necessity of a team approach to provide the best care to affected children and support for their families. professor oyewale tomori from nigeria highlighted the angolan yellow fever outbreak, the largest in 30 years, that spread to neighboring countries, and quite worrisomely via travelers to asia. despite the long availability of an effective vaccine, the shift of hotspots from west to central africa, failures of vaccination policy and vaccine shortages combined to produce this global threat. rapid urbanization, mass population movements, climate change, and resistance to pesticides and available treatments increase the risk of epidemics in the future, argued dr. mercedes tatay from doctors without borders. current strategies to prevent major outbreaks of disease show limited success. epidemics continue to occur with devastating consequences for less developed countries. she argued that in reality, not all epidemics are viewed equally. the global health security concept at the heart of the international health regulations defines protection against a threat as the main trigger for international action. she concluded that emergency response needs to be prioritized not in competition with long-term goals such as public health surveillance and health systems strengthening. west africa's ebola epidemic was unprecedented with more than 28,000 reported cases, more than 11,000 reported deaths and more than 10,000 survivors. in response to the epidemic, four global commissions were established to critically evaluate the national and global response and to enhance preparedness to prevent, detect, and respond to future infectious disease threats. 1 professor [ 1 7 _ t d $ d i f f ] daniel lucey summarized the commissions' recommendations including the importance of strengthening national health systems, consolidating and strengthening world health organization (who) emergency and outbreak response activities, and enhancing research and development. who agreed to one of the most profound transformations in the organization's history by establishing a new health emergencies programme. the programme is designed to add operational capabilities for outbreaks and humanitarian emergencies to complement its traditional technical and normative roles. similarly, the recommendations of the review committee on the role of the international health regulations (ihr) was focused on the implementation aspects of the ihr. the implementation of a vaccine trial during an epidemic was discussed by dr. barbara mahon, us cdc lead for the sierra leone trial to introduce a vaccine against ebola (strive), a phase 2/3 trial sponsored by cdc in collaboration with the college of medicine and allied health sciences, university of sierra leone, and the ministry of health and sanitation. 2 the trial was designed to accelerate introduction and use of the recombinant vesicular stomatitis virus zaire ebola vaccine (rvsv-zebov) among at-risk people in sierra leone with concurrent evaluation of the efficacy and safety of the vaccine. she talked about the challenges implementing strive in the face of limited infrastructure, high community concern, and changing epidemiology. preliminary analysis of safety data indicated no vaccine-related deaths or other serious adverse events; although strive did not produce an estimate of vaccine efficacy because of low case frequency as the epidemic was controlled, data on safety and immunogenicity will support decisions on licensure of rvsv-zebov. the importance of open data sharing during epidemics and ethical challenges of using big data for early detection and prevention were discussed during a roundtable discussion moderated by professor effy vayenna who was joined by experts from the who, the wellcome trust and the centre on global health security (chatham house, london). the importance of communicating to the press and public during an outbreak and how to best communicate uncertainty was reviewed by helen branswell of the us-based stat news. she noted the importance of building rapport between public health authorities, scientists and journalists prior to the onset of an outbreak. dr. edward rubin presented advances in diagnosis and how the genomic revolution and acceleration of dna sequencing throughput allows us to increasingly consider unbiased metagenomic analysis as a tool to detect emerging diseases. the lack of therapeutics for the next viral epidemic were discussed by professor paul tambyah. in a separate session, the challenges posed by climate change on infectious disease outbreaks and how to best prevent and track diseases in mobile populations were discussed. dr. joel montgomery stated that while researchers are understanding how changes in temperature, precipitation and vegetation phenology impact malaria and certain arbovirus vectors, relatively less attention has been paid to the impact of climate change on neglected tropical diseases (ntd) and the challenges migration may pose to ntd elimination efforts. the ''tracking emerging diseases'' session highlighted innovations in disease surveillance and the increasing role of informal sources to detect unusual health events early. dr. mark smolinski, the chief medical officer and director of global health threats at the skoll global threats fund described a transformation of citizen engagement in public health through systems that empower users to directly report on symptoms of disease via email and smartphone technology. these new and innovative systems provide early warning for outbreaks and other health and safety issues, even before users seek health care, and have the potential to transform rapid risk assessment and epidemiological studies. further exploring the role of informal data sources to detect outbreaks earlier, professor anna thorner discussed how physician searches using uptodate -an evidence based, online, clinical decision making tool that is continuously updated -can be used to detect outbreaks early on before cases are reported and confirmed. the european migrant crisis has raised questions regarding the re-emergence of infectious diseases and the monitoring and screening of migrants arriving in europe and elsewhere. in a session presented in collaboration with the european society for clinical microbiology and infectious diseases, physicians from germany and turkey, both countries with a recent high influx of refugees, talked about their countries' challenges and experiences in providing health care and preventive services to refugees and asylum seekers. they called for uniform screening practices and early access to primary and specialized healthcare and emphasized the need for appropriate vaccination coverage. they were joined by colleagues from italy and switzerland discussing the related topics of disease surveillance and tracing antibiotic resistance in mobile populations. [ 1 3 _ t d $ d i f f ] antimicrobial resistance in the one health context antibiotic resistance is a major global public health concern and resistance is growing faster than new drugs are being developed. antibiotic resistance needs to be understood in the one health context. the importance of the food chain as a source for emergence and spread of antimicrobial resistance between animals and humans was highlighted in a nation-wide study in lebanon. dr. ghassan matar described a direct transfer of resistant determinants in bacterial clones from animal food products to humans. but understanding antimicrobial resistance is expanding even further, from human and animal antibiotic use to the human influence on resistance in the environment. dr. ursula theuretzbacher noted that the link between the animal and human sector was well studied and led to policy changes in some parts of the world. such regulatory initiatives are still missing in the environmental field which is usually not included in the one health approach to tackle the global resistance problem. the direct release of multidrug resistant bacteria from healthcare settings, antibiotic manufacturing facilities and animal farms into the environment as well as the pollution of the environment with high concentrations of antibiotics create a dangerous resistance reservoir. drs. peter daszak and dennis carroll closed imed 2016 with a plenary talk on the proposed ''global virome project'', a global initiative to map all of the planet's viral threats over the next 10 years which would represent a dramatic step towards knowing our viral enemy. researchers so far have identified only the tip of the iceberg of viral threats and even fewer of these viruses had effective vaccines or antiviral agents developed. the speakers presented viral discovery data estimating that there are around 500,000 yet-to-be-discovered viral species capable of posing public health threats circulating in the world. they discussed the resources and effort it will take to realize this vision and the technical advances that will make it possible. toward a common secure future: four global commissions in the wake of ebola implementing an ebola vaccine study -sierra leone key: cord-258669-ubw6mdzi authors: colebunders, robert; siewe fodjo, joseph nelson; vanham, guido; van den bergh, rafael title: a call for strengthened evidence on targeted, non-pharmaceutical interventions against covid-19 for the protection of vulnerable individuals in sub-saharan africa date: 2020-08-27 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.060 sha: doc_id: 258669 cord_uid: ubw6mdzi since many sub-saharan african countries started easing their lockdown measures, covid-19 cases have been on the rise. as covid19 transmission may be difficult to stop in these settings, we propose to complement the existing covid-19 prevention strategies aiming at reducing overall transmission with more targeted strategies to protect people at risk for severe covid-19 disease. we suggest investigating the feasibility, acceptability, and efficacy of distributing covid-19 prevention kits to households with persons at increased risk for severe covid-19 disease. a curious imbalance exists between the research and development (r&d) efforts dedicated to pharmaceutical versus non-pharmaceutical interventions in outbreak control. the scientific output as well as the associated r&d investments for pharmaceutical interventions are often a factor higher than those for non-pharmaceutical interventions, even though the latter commonly represent a cornerstone of outbreak control. this seems no different in the case of the coronavirus disease-2019 j o u r n a l p r e -p r o o f pandemic: at the time of writing, a pubmed search indicates that the number of published peer-reviewed articles on covid-19 and treatment/vaccination is approximately double that of covid-19 and containment/prevention. pharmaceutical interventions such as treatment or vaccination benefit -rightly -from calls for innovation, extensive investigations, rigorous monitoring and evaluation, and the best that evidence-based medicine has to offer. in contrast, while nonpharmaceutical interventions such as physical distancing, lockdowns, contact tracing, facemask promotion, and others have been implemented almost ubiquitously as a measure to stem covid-19 transmission, they have tended to be implemented as a blanket approach, with limited monitoring and evaluation, and limited generation of evidence to adapt strategies as they go along. here, we call for the generation and strengthening of evidence to guide non-pharmaceutical interventions for covid-19, which we illustrate with a practical proposal for assessing the impact of targeted protection of at-risk individuals in settings in sub-saharan africa. the sub-saharan africa region was touched relatively late by covid-19, with the first case occurring in nigeria in late february 2020 (nigeria centre for disease control 2020). while implementation of general preventive measures in sub-saharan africa may have slowed down the pandemic, it seems it cannot be stopped: by august 14 th , there were more than one million covid-19 cases in africa, with more than 24,000 deaths (africa cdc 2020). as covid-19 diagnostic capacity remains limited in the region, the reported numbers of covid-19 cases and deaths are likely an underestimation of the true disease burden. moreover, since many african countries are now easing lockdown measures, the number of covid-19 cases is likely to increase rapidly. a sharp increase has already been observed in south africa, which now accounts for more than 50% of the continent's total confirmed cases (who 2020). despite the increasing community spread of covid-19 in sub-saharan africa, mortality rates reportedly remain low in most countries. this may be related to the relatively younger demographic j o u r n a l p r e -p r o o f in the region: the proportion of persons age 60 and over was estimated to be 4.7% in 2005 and is expected to rise to 5.5% in 2030 (velkoff and kowal 2006) , compared to approximately 20% in e.g. western europe currently. nevertheless, the region is home to more than 50 million elderly (aged 60 and over) (united nations 2019), who can be considered at elevated risk for severe infection. additionally, the continent has seen a steady increase in non-communicable diseases (ncd) such as diabetes (ojuka and goyaram 2014) and hypertension (bigna, noubiap et al. 2017) , which have been linked to covid-19 severity (rastad, karim et al. 2020 , zhou, chi et al. 2020 , and additionally carries a high burden of infectious diseases such as hiv and tuberculosis, which have been speculated to represent particular risk factors for severe covid-19 infection as well (davies 2020 ). with covid-19 gaining ground in sub-saharan africa and the sizeable population of vulnerable individuals at risk of severe covid-19, the often already-fragile health systems in many african settings risk being dramatically outpaced by the pandemic. at the onset of the covid-19 pandemic, lockdowns were swiftly recommended as strategy for covid-19 prevention. such interventions were typically modelled on the covid-19 outbreaks in high-income countries and were subsequently replicated in other settings, such as sub-saharan africa (hodgins and saad 2020) . concerns have however been raised that the pandemic follows very different trajectories in different contexts, and that a "one size fits all" approach for nonpharmaceutical interventions may not be appropriate, as the risk-benefit balance of such interventions may vary across settings (hodgins and saad 2020, van damme, dahake et al. 2020) . although the early implementation of lockdown measures for covid-19 control may have contributed to the (initially) low mortality observed in most sub-saharan africa countries, the collateral damage resulting from this strategy is becoming increasingly apparent. lockdown measures have resulted in major economic losses, loss of jobs (yaya, otu et al. 2020) , increase of poverty (yaya, otu et al. 2020) , food shortages (mclinden, stover et al. 2020) , mental health problems (guessoum, lachal et al. 2020 , joska, andersen et al. 2020 , domestic and other forms of violence (joska, andersen et al. 2020) , and disruption of health services through drug shortages and an overall negative impact on the quality of non-covid-19 healthcare. moreover, it is expected that post-lockdown, there will be an increased burden of malaria, tuberculosis (nghochuzie, olwal et al. 2020 ) and of neglected tropical diseases resulting from the suspension of control programs. in addition to the fact that lockdown measures are more detrimental to those with the least resources, they are unlikely to be sustainable for the stretch of time required to fully curtail covid-19 transmission in the long run. we therefore propose to complement the extant containment measures in sub-saharan africa with more targeted protection strategies, aiming at protecting people at risk of severe covid-19 disease. a targeted strategy may be more efficient to decrease covid-19 related mortality and to prevent health systems from being overwhelmed by cases in need of resource-demanding intensive support. if implemented together with the general measures to limit the spread of covid-19 in the population such as physical distancing, universal facemask use and frequent handwashing, such a strategy may provide authorities with the means to selectively relax population-wide measures in favour of these more targeted approaches. protecting persons at risk of severe covid-19 disease may however be challenging. in high-income countries, where inter-generational mixing within households is less common and where many elderly reside specifically in long-term care facilities, protection was ostensibly straightforwardhowever, few countries failed to safeguard these populations (ecdc public health emergency team, danis et al. 2020 , miller 2020 . in sub-saharan africa, where elderly family members generally live together with the rest of the family or in close contact with them, this challenge may be further compounded. additionally, one's ncd status may be less well documented in african contexts, j o u r n a l p r e -p r o o f prohibiting self-identification as vulnerable. we propose to develop and test different targeted covid-19 prevention strategies adapted to the sub-saharan african context. one strategy could be to distribute covid-19 prevention kits to households with persons at increased risk for severe covid-19 disease. hygiene kits or prevention kits have been used successfully in other outbreaks, commonly for fecoorally transmitted diseases such as cholera or ebola, as stopgap measure when population-wide prevention tools. we surmise that basic kit items will include fabric facemasks, soap, water storage capacity, alcohol-based hand gel, and health education materials. these materials should ideally cover topics such as respecting at least 1.5 m distance from the person at risk for severe covid-19 disease, always wearing a facemask when interacting with these persons, having these persons wear a facemask when in the company of others, and limiting human interactions with these persons until covid-19 is eliminated. moreover families could be given access to a phone help-line for more personal advice and support. experience with such kits exists, but needs to be contextualised to covid-19 (lewnard, ndeffo mbah et al. 2014 , yates, allen et al. 2017 , ali, benedetti et al. 2020 , d'mello-guyett, greenland et al. 2020 . different ways to identify families with persons at risk for severe disease should be explored. identification could be integrated within a contact tracing programme, whereby a symptomatic person suspected to have covid-19 is investigated as to whether there is a person at risk for severe covid-19 disease in her/his household. this approach may be logistically easier to implement, as it j o u r n a l p r e -p r o o f would allow centralised distribution of kits, but risks coming too late as the person at risk could already be infected. in communities where there is high ongoing covid-19 transmission, it may be preferable but more costly to offer prevention kits to all those with a household member at risk, irrespective of any suspicion of active covid-19 in the family, since it is becoming increasingly clear that asymptomatic infected subjects can also spread the infection. such an approach could be aided by demographic records that indicate the ages of residents in the different households and/or medical records from local ncd programmes, and safe and efficient distribution models to realise this approach would need to be tried and tested. another entry point for the distribution of kits could be clinics attended by persons with co-morbidities such as diabetes, hypertension, hiv and tuberculosis. in rural areas, community health workers could play a key role in identifying vulnerable persons, health education and distribution of kits. who should be the focus of the targeted intervention needs to be investigated in each setting taking into account the phase of the covid-19 epidemic, the commonness and types of vulnerable people, whether they are known in the community, the ability of the local community health workers to recognise vulnerable people, the cultural context, and the financial resources. the easiest way is to consider all persons older than 60 years at risk for severe covid-19 disease. recently, a frailty scale was shown to be more predictive of covid-19 disease outcome than age and co-morbidities (hewitt, carter et al. 2020) . however, it needs to be investigated whether community health workers will be able to categorize persons using such a scale and how much resources (time, finances) this will require. formative research will be necessary to explore the composition of the prevention kit; this will depend on local needs and resources. the distribution of the kits will need to be pilot-tested for feasibility and acceptability. to minimize cost, we recommend large scale local production of fabric face masks. an important component of the intervention would be the counselling of the families by the community health workers. while the exact cost for the production and dissemination of the j o u r n a l p r e -p r o o f prevention kits (including the incentives for the community health workers) may be difficult to evaluate, the proposed targeted approach appears to be more cost-beneficial than all-inclusive strategies such as providing face masks to the entire population and enforcing strict contingency measures, with the associated economic backlash. this model of targeted intervention should be compared with interventions focusing mainly on decreasing overall covid-19 transmission. there is thus an urgent need to upscale research capacity, in order to appropriately address these questions. currently, a large proportion of the covid-19 research funding for the prevention covid-19 transmission is being directed towards the development of a vaccine. it is however unlikely that an effective vaccine will be available very soon in all covid-19 transmission foci in sub-saharan africa. therefore we recommend that well-designed studies, including randomised trials, be planned and conducted in sub-saharan africa to identify the most cost-efficient ways to decrease the covid-19 disease burden, while at the same time mitigating collateral damage of prevention measures. hygiene kits may be one such measure worthy of investigation. in collaboration with somalian investigators, we have submitted a research proposal for a cluster randomised trial among camps for internally displaced persons in somalia to compare a targeted covid-19 prevention programme to reduce severe covid-19 related disease and mortality with a standard covid-19 prevention program to reduce overall covid-19 transmission. for the moment, such a targeted intervention using prevention kits in is only possible in somalia with external funding. however, we hope that if a significant difference in severe disease and mortality is shown, governments, non-governmental organisations and funding agencies will try to scale up and sustain similar interventions in other settings. j o u r n a l p r e -p r o o f distribution of household disinfection kits during the 2014-2015 ebola virus outbreak in monrovia, liberia: the msf experience prevalence and etiologies of pulmonary hypertension in africa: a systematic review and meta-analysis distribution of hygiene kits during a cholera outbreak hiv and risk of covid-19 death: a population cohort study from the western cape province, south africa high impact of covid-19 in long-term care facilities, suggestion for monitoring in the eu/eea adolescent psychiatric disorders during the covid-19 pandemic and lockdown the effect of frailty on survival in patients with covid-19 (cope): a multicentre, european, observational cohort study will the higher-income country blueprint for covid-19 work in low-and lower middle-income countries? covid-19: increased risk to the mental health and safety of women living with hiv in south africa dynamics and control of ebola virus transmission in montserrado, liberia: a mathematical modelling analysis hiv and food insecurity: a syndemic amid the covid-19 pandemic protecting and improving the lives of older adults in the covid-19 era pausing the fight against malaria to combat the covid-19 pandemic in africa: is the future of malaria bleak? first case of corona virus disease confirmed in nigeria increasing prevalence of type 2 diabetes in sub-saharan africa: not only a case of inadequate physical activity risk and predictors of in-hospital mortality from covid-19 in patients with diabetes and cardiovascular disease world population prospects the covid-19 pandemic: diverse contexts; different epidemics-how and why? aging in sub-saharan africa: the changing demography of the region. aging in sub-saharan africa: recommendation for furthering who coronavirus disease (covid-19) dashboard short-term wash interventions in emergency response: a systematic review globalisation in the time of covid-19: repositioning africa to meet the immediate and remote challenges obesity and diabetes as high-risk factors for severe coronavirus disease 2019 (covid-19) the authors have no conflict of interest no ethical approval is required key: cord-253102-z15j8izi authors: ross, allen g.p.; crowe, suzanne m.; tyndall, mark w. title: planning for the next global pandemic date: 2015-08-04 journal: int j infect dis doi: 10.1016/j.ijid.2015.07.016 sha: doc_id: 253102 cord_uid: z15j8izi in order to mitigate human and financial losses as a result of future global pandemics, we must plan now. as the ebola virus pandemic declines, we must reflect on how we have mismanaged this recent international crisis and how we can better prepare for the next global pandemic. of great concern is the increasing frequency of pandemics occurring over the last few decades. clearly, the window of opportunity to act is closing. this editorial discusses many issues including priority emerging and re-emerging infectious diseases; the challenges of meeting international health regulations; the strengthening of global health systems; global pandemic funding; and the one health approach to future pandemic planning. we recommend that the global health community unites to urgently address these issues in order to avoid the next humanitarian crisis. the west african ebola virus pandemic has shown us yet again that the world is ill prepared to respond to a global health emergency. this follows similar statements that were made after the h1n1outbreak in 2009 that ''the world is ill prepared to respond to a severe influenza pandemic or to any similar global, sustained and threatening public health emergency''. 1 our response to the ebola zoonotic 'spillover' was delayed and as a result 11,158 people lost their lives in nine countries. 2 the direct financial cost of the ebola pandemic was estimated to be in the vicinity of six billion us dollars and global economic losses over 15 billion dollars. 3 clearly there are lessons to be learnt from the ebola outbreak. in 2005, following the severe acute respiratory syndrome (sars) pandemic, the international health regulations (ihr) were modified. while two thirds of the 194 world health assembly countries have failed to comply with the regulations as of 2015, and for the one third who say they did, there are serious concerns about the reliability of their self-assessment. 4 now, with liberia declared free of ebola and declining incidence in sierra leone and guinea, these same regulations are once again being revisited after more than a decade. 4 is this a futile exercise and should the ihrs be abandoned if they cannot be enforced by who and fulfilled by the world health assembly (wha) member nations? the national health systems in west africa, and for most low and middle income countries (lmics), would not meet ihr standards (despite claims by some member wha nations) and it is unlikely that following the ebola pandemic much will change. many have stated that who failed to respond to the current ebola epidemic in a timely manner 4 but even if they did, would the outcome have been really that different? there were no drugs or vaccines available to treat and prevent the disease, thus quarantine, isolation and safe burials were the primary methods utilized to halt the spread of disease and were initiated by the afflicted nations themselves. 5 it typically takes years if not decades to develop a vaccine or drug that will have public health impact. one only has to look at the countless billions that have been spent on trying to develop a vaccine for hiv, thus far without success. moreover, weak, malnourished, immunosuppressed populations living in poverty with little or no hygiene, sanitation or running water will always be highly susceptible to new emerging or reemerging infectious diseases. 6 at 'ground zero' of the ebola epidemic it was believed that in 2013, hungry children living in the remote guinean village of meliandou killed and ate infected fruit bats. 7, 8 thus, what can realistically be done to prevent and contain future national epidemics from becoming global pandemics? we discuss a number of issues that urgently need to be addressed in order to plan, and possibly prevent, the next global pandemic. if one looks at the history of emerging or re-emerging infectious disease pandemics globally, on average they have appeared every decade but now, worryingly, the frequency between pandemics seems to be disturbingly shorter as evident with severe acute respiratory syndrome ( in order to mitigate human and financial losses as a result of future global pandemics, we must plan now. as the ebola virus pandemic declines, we must reflect on how we have mismanaged this recent international crisis and how we can better prepare for the next global pandemic. of great concern is the increasing frequency of pandemics occurring over the last few decades. clearly, the window of opportunity to act is closing. this editorial discusses many issues including priority emerging and reemerging infectious diseases; the challenges of meeting international health regulations; the strengthening of global health systems; global pandemic funding; and the one health approach to future pandemic planning. we recommend that the global health community unites to urgently address these issues in order to avoid the next humanitarian crisis. international journal of infectious diseases j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / i j i d human/host/reservoir interaction. 10 weak malnourished populations in lmics serve as the breeding grounds for future pandemics ( figure 1 ). for example, in metro manila, the most densely populated city in the world, approximately six million people live in slums with no piped water or toilets. according to who, 137 million people in urban centres have no access to safe drinking water and over 600 million lack sanitation. 10 the un predicts that the world's urban population will double to over six billion by 2050 and most of the increase in density will occur in lmics. 10 population density is directly correlated with the rate of transmission of respiratory and faecal-oral pathogens (e.g. mycobacterium tuberculosis, influenza, cholera, rotavirus, helminths). 10 between 1940 and 2004 there were 335 emerging infectious disease (eid) origins reported globally. 9 figure 2 illustrates some of the most recent eid epidemics. eids are primarily zoonotic (60%), originating in wildlife populations (e.g. hiv, sars, ebola, west nile virus, lyme disease) but bacterial pathogens have become increasingly of concern due to antibiotic resistance especially in the developing world. 9, 11 multidrug-resistance (mdr) to mycobacterium tuberculosis, streptococcus pneumoniae and staphylococcus aureus are a global concern and gram-negative bacteria resistance to b-lactams is widespread. 11 drug resistance to enteropathogens has also become a major global health challenge. mdr salmonella enterica typhi and s. enterica paratyphi are common in asia and sub-saharan africa, and there are increasing reports of reduced susceptibility to fluoroquinolones. 12 campylobacter jejuni resistance to fluoroquinolones has become a concern in southeast asia, with rates of resistance of 80% reported from thailand. 12 viral pathogens (e.g. ebola, makona variant (ebov), mers-cov, h1n1) are also of concern due to their high rates of nucleotide substitution, poor mutation error-correction rate ability and capacity to quickly adapt to human hosts. 9 table 1 displays some potentially pandemic pathogens that should be under active global surveillance. the current outbreak of mers-cov in south korea is of grave concern given the case fatality rate is over 10%. surveillance of zoonotic diseases is largely based on detecting illnesses in humans who often serve as the sentinel species and dead-end hosts. 13 apart from rabies, most national surveillance systems in the world do not monitor zoonotic diseases appearing in wildlife, yet 72% of zoonotic eids (e.g. anthrax, nipah virus, hantavirus, type a influenza, sars, mers-cov, ebola) come from this source. 9, 13 many rna viruses have emerged and dispersed globally such as chikungunya virus, west nile virus and dengue virus. these three arboviruses alone have morbidity and mortality rates that far exceed those of the combined rates of sars, ebola and mers-cov. 14, 15 thus, eid discovery efforts need to be directed toward reservoirs and vectors at the human-animal interface. 16 the integration of human, veterinary, and agricultural medicine, as proposed by the 'one health' approach, should result in earlier warning of eids and provide us with a better opportunity to respond to potential spill-over threats. 13, 17 moreover, targeting surveillance to regional hotspots of eids provides an evidencebased rationale for more appropriate allocation of global resources. 16 the 2014 outbreak of ebola once again tested the revised 2005 ihr. according to gostin and friedman (2015) ''who fell short of its leadership responsibilities, and the ihr -the governing legal framework -displayed deficiencies''. 3 the three west african countries involved (guinea, liberia, sierra leone) in the pandemic failed to comply with the ihrs capacity-building mandate and, to date, two thirds of wha member countries have failed to comply with the same regulations. 3, 4 of the one third of the wha member nations that said they did comply, there has been no evaluation to verify their claims. 3, 4 like the outbreak of h1n1 in 2009, the response raises questions regarding the extent to which the ihr can serve as a framework for global pandemic responses. 3, 4, 18 if the wha member nations (194) do not take the ihr core capacity-building requirements of disease surveillance, reporting, and response seriously, then why continue to use them as an international framework? in reality wha member nations from lmics see the regulations as an enormous obligation primarily developed to protect the health and welfare of developed nations. 3, 18 during the ebola outbreak, controversy arose when american and spanish nationals were preferentially chosen to receive the experimental drug zmapp over west african nationals. 19 moreover, when foreign medical staff became infected they were flown home for what was deemed superior medical care. clearly these ethical issues, which are well known by the wha member representatives, will impact on future ihr compliance. furthermore, member nations from lmics do not have the national capacity to adhere to ihr, given they have very weak infrastructure and poorly financed health systems. 3 lmics must be given considerable financial and capacity building assistance or they will be unable to comply. these massive inequities must be addressed if we are to plan appropriately for the next pandemic. for most countries in the developing world it is difficult to improve their health systems to a standard that is similar to that of high-income countries. moreover, as mentioned, most lmic countries will not be able to establish core ihr capabilities without considerable donor support and international assistance for training, creating the necessary laboratory infrastructure for prompt diagnosis, and the technology required for 'real-time' reporting of epidemics. 20 point of care screening tests for use in community health posts are increasingly available for rapid diagnosis of emerging pathogens and will shorten the time from presentation to treatment. however improvements and access to diagnostic technologies will need to be supported by the capacity to interpret and act on the findings. presently limited health-care dollars are spent on running tertiary national hospitals with little, or none, spent on preventive services, disease control or epidemic preparedness. however, most countries do have offices or departments for communicable disease control with the number of staff engaged in such full-time activities varying considerably. at the district/municipal level most developing countries have medical health officers and at the community level a considerable human resource of community health workers (chws). gostin and friedman (2015) have proposed a new global health framework with robust national health systems at its foundation and an empowered who at its apex. 3 however, who has failed to provide the necessary leadership to coordinate global health emergencies on the ground and adequately support wha member nations to develop core ihr capacities. in september 2014, the un assumed leadership of the ebola response and created the un mission for emergency ebola response (unmeer), the first un mission to respond to public health emergencies. 3 in contrast with ihr recommendations, security council resolutions are legally binding for member countries. 3 we now propose a new un centre for disease control (un cdc), potentially based in new york, to serve at the apex of a new global health framework with a number of new and existing regional cdcs reporting directly to it (figure 3) . a proposed structure might be: national cdc departments reporting to their regional cdcs, and provincial/district/municipal cdc departments reporting to their national cdcs with community health workers at local health centres reporting to their municipal health officers. in sum, at the apex of our proposed global health framework would sit a new un cdc with security council authority and at the foundation, chws in local health centres. chws have transformed the health-care systems of many developing nations including bangladesh, india, ethiopia, and malawi and are absolutely crucial for future global security. 21 on october 10 th 2014, world bank president, dr jim yong kim, has proposed a new pandemic emergency facility (pef). 22 as stated on their website ''the world bank group is playing a lead role in conceptualizing the facility, working in coordination with international organizations, including the who, the private sector and other development partners. pef is a global financing facility that would channel funds swiftly to governments, multilateral agencies, ngos and others, to finance efforts to contain dangerous epidemic outbreaks before they turn into pandemics. financing from the pef will be linked to strong country-level epidemic and pandemic emergency preparedness plans, thereby incentivizing recipient governments and the international community to introduce greater rigor and discipline into crisis preparedness and reduce the potential for moral hazard. the pef is expected to cover a range of response activities such as: (i) rapid deployment of a trained and ready health care work force; (ii) medical equipment, pharmaceuticals and diagnostic supplies; (iii) logistics and food supplies; and (iv) coordination and communication. the pef would 22 if the who contingency fund (100 million us dollars) and the world bank pandemic emergency facility cannot be utilised to strengthen national health systems in lmics in order to meet ihrs core capabilities, then how can this be achieved? a multi-billion us dollar international health system fund has been proposed 3 but considerable funding from both the private and public sector will need to be secured if the fund is to be successfully launched. the g20, the european union, and philanthropic organizations will need to contribute. the implementation and monitoring of such funds at the national level will have to be carefully scrutinised and audited if the core capacities of the ihrs are to be achieved and maintained. ultimately lmic nations themselves will need to allocate health care dollars toward health prevention and epidemic planning. for many lmics this is not a priority and they are ill prepared to respond to epidemics on their own soils. building national capacity is the rate limiting step for global health security. if the international community fails to support this capacitybuilding initiative then this puts the world in a precarious situation with regard to future pandemics. it is well known in management circles that 'if one fails to plan then one should plan to fail'. with regard to pandemic planning, if we fail to build national epidemic capacities in lmics then we should plan to deal with a global pandemic in the not too distant future. however, in order to build such national capacity it will take considerable international political will that at the moment seems to be lacking. instead of allocating huge resources that 'react' to pandemics, funds must be earmarked to 'prevent' pandemics. this would include building national capacities of lmics and smart surveillance of eids in identified hotspots in the tropical and subtropical world. what are the likely organisms to cause a future pandemic and where will they originate from? zoonosis from wildlife represents the most significant global health threat of our time yet little funds are spent monitoring and identifying new zoonotic pathogens originating in wildlife. clearly a 'one health' approach is the way forward. pandemic preparedness and response-lessons from the h1n1 influenza of 2009 a retrospective and prospective analysis of the west african ebola virus disease epidemic: robust national health systems at the foundation and an empowerd who at the apex report of the ebola interim assessment panel. who reference number: a68/25 are we ready for a global pandemic of ebola virus? an audacious goal: the elimination of schistosomiasis in our lifetime through mass drug administration bat-filled tree may have been ground zero for the ebola epidemic outbreak of ebola virus disease in guinea: where ecology meets economy global trends in emerging infectious diseases urbanisation and infectious diseases in a global world surveillance for antimicrobial drug resistance in under-resourced countries enteropathogens and chronic illness in returning travellers surveillance and control of zoonotic agents prior to disease detection in humans factors responsible for the emergence of arboviruses ecology of zoonoses: natural and unnatural histories prediction and prevention of the next pandemic zoonosis the economic value of one health in relation to the mitigation of zoonotic disease risks the revised international health regulations: a framework for global pandemic response ebola in west africa: learning the lessons global health security: the wider lessons from the west african ebola virus disease epidemic health inequalities and infectious disease epidemics: a challenge for global health security the world bank. global pandemic emergency facility key: cord-306682-01q775up authors: vijgen, leen; keyaerts, els; zlateva, kalina; van ranst, marc title: identification of six new polymorphisms in the human coronavirus 229e receptor gene (aminopeptidase n/cd13)() date: 2004-06-22 journal: int j infect dis doi: 10.1016/j.ijid.2004.03.004 sha: doc_id: 306682 cord_uid: 01q775up objective: human aminopeptidase n (apn/cd13/anpep) has been identified as the receptor for human coronavirus (hcov) 229e. in this study, we analyzed the region of the apn gene that encodes a stretch of amino acid residues, essential for its hcov-229e receptor function (amino acids 260–353). methods: full-length apn exon 3, intron 3 and exon 4, was pcr-amplified and sequenced in dna samples from 100 unrelated caucasian belgian healthy volunteers. results: we identified seven polymorphisms, including four intron 3 and three exon 4 variations. apart from the already known c956t exon 4 mutation, the six other polymorphisms have not yet been described. the most prevalent apn variations in this population (c956t leading to an alanine to valine substitution, g978t, g987a and intron3-c389t) always occurred together at an allele frequency of 8.5%. haploid dna sequencing demonstrated the presence of these four variations on the same allele. three polymorphisms in intron 3, intron3-g395c, intron3-c86t, and intron3-c429t, were identified with an allele frequency of 3.5%, 1% and 0.5% respectively. five haplotypes were identified in the population of 100 individuals. conclusion: these results demonstrate that there is a relatively broad spectrum of variations in the apn domain critical for coronavirus binding. the nucleotide sequence reported here has been submitted to the genbank database with the following accession number: af527789. coronaviruses are large, enveloped, single-stranded, positive-sense rna viruses, with a genome size of approximately 30 kb. human coronaviruses (hcov), with two known serogroups designated oc43 and 229e, are an important cause of upper respiratory tract illnesses, and are also implicated in diseases involving the digestive and the central nervous system. 1 after the recent sars outbreak and the discovery of a new coronavirus (sars-cov) as the causative agent, the importance of coronaviruses in human medicine can no longer be neglected. 2 as a first step in viral entry into the cell, human coronavirus 229e (hcov-229e) attaches, in a species-specific manner, to aminopeptidase n (apn/cd13/anpep). 3 in other species apn is also used as a receptor by the hcov-229e related group i coronaviruses (porcine transmissible gastroenteritis virus, porcine epidemic diarrhea virus, feline infectious peritonitis virus and canine coronavirus). 4, 5 although human apn had also been suggested as a putative receptor for the spike glycoprotein of the sars-associated coronavirus (sars-cov), it has now been proven that not apn but angiotensin-converting enzyme 2 is a functional receptor for sars-cov. 6, 7 the receptor for human coronavirus serotype oc43 (hcov-oc43) is still unknown, although evidence has been presented that 9-o-acetylated sialic acid is used as a receptor determinant for infection of human cells. 8 apn is a type ii glycoprotein that belongs to the family of membrane-bound metalloproteases. the 150 kda apn glycoprotein (ec 3.4.11.2) is composed of 967 amino acids and is expressed in a variety of tissues including cells of the monocytic and granulocytic lineage, synaptic membranes of the central nervous system, and intestinal, lung and kidney epithelial cells. 9 a soluble form of apn is reported to be present in human plasma. 10 the physiological role of apn includes the conversion of oligopeptides in the small intestinal lumen into amino acids, and an involvement in the degradation of regulatory peptides in other tissues such as the kidney and the brain. 9 the human apn gene has been mapped to chromosome 15q25-26, and the coding part of the gene is divided in 20 exons. 11, 12 expression of apn is regulated by two different promoters, separated by an 8 kb intron, leading to the formation of two transcripts that only differ in their 5 non-coding region. the epithelial promoter is located close to the coding part of the gene and is active in enterocytes and other epithelial cells, while the more upstream myeloid promoter is mainly active in myeloid cells. 13 two splice variants in which exon 3 and exon 14 were lost, have recently been identified, resulting in both cases in a carboxy-terminal truncated protein. 14 several applications of apn in therapy and diagnosis have been described. apn/cd13 is frequently used in the characterization and typing of leukemia or lymphoma cells, as apn/cd13 is expressed on stem cells and during most developmental stages of myeloid cells. 15 it has recently been demonstrated that apn/cd13 is both a receptor for tumor homing peptides and a functional regulator of angiogenesis, implicating a role for apn/cd13 as a target for anti-angiogenic therapy and tumor targeted drug delivery. 16, 17 apn has also been shown to mediate human cytomegalovirus (hcmv) infection. 18 the inhibition or neutralization of hcmv infection by soluble apn implicates the possibility of using soluble apn as an antiviral agent. the domain of human aminopeptidase n that is essential for its hcov-229e receptor activity has been assigned to apn amino acids 260-353, with a critical stretch of eight residues (amino acids 288-295). 19, 20 this region is encoded by the major part of apn exon 3, whole exon 4 and a small part of apn exon 5 (nt 802-1083, hapn mrna, genbank accession number x13276). in this study we examined whether polymorphisms could be detected in the hcov-229e binding domain of apn in a caucasian population of 100 unrelated, healthy individuals, assuming that these mutations could be of importance in hcov-229e attachment to human cells. the study involved a caucasian population of 100 healthy, unrelated individuals from the region of flanders, the northern part of belgium. informed consent was obtained from all participants and the study had the approval, based upon the guidelines from the world medical association's declaration of helsinki, of the ethics board of the university of leuven. 21 dna samples were collected through a non-invasive 'swish-and-spit' technique. genomic dna was acquired from oral epithelial cells, by rinsing the oral cavity with a 0.9% saline solution, after which dna was extracted using an alkaline lysis procedure. 22 an 871 bp fragment, encompassing exon 3, intron 3 and exon 4 of the aminopeptidase n gene, was amplified by polymerase chain reaction (pcr), using 5 -tgcttcccaaaggtgagtgg-3 as the forward primer and 5 -ccattggcaggatgaactcc-3 as the reverse primer (genbank accession number ac018988). pcr amplification was performed in a volume of 50 l reaction mix, with a concentration of 0.2 m of forward and reverse primer, 0.2 mm of nucleotides, 1.5 mm of mgcl 2 and 1 unit of taq polymerase (applied biosystems/roche molecular systems, belgium) at ph 9. pcr conditions were composed as follows: an initial denaturation at 95 • c for five minutes, then 40 cycles of 30 seconds at 95 • c, 30 seconds at 57 • c and 35 seconds at 72 • c, and a final elongation at 72 • c for seven minutes. the amplification reaction was performed in a geneamp ® pcr system 9700 thermal cycler (applied biosystems, foster city, ca, usa). the resulting pcr products were visualized after electrophoresis, on an ethidium bromide-stained polyacrylamide gel. after purification of the pcr products with the qiaquick pcr purification kit (qiagen, westburg, the netherlands), the purified products were cycle sequenced in forward and reverse direction using the abi prism bigdye terminator cycle sequencing ready reaction kit (applied biosystems, foster city, ca, usa). besides the pcr primer set, two additional primers, a forward: 5 -ctgccccaggatcaaacagg-3 and a reverse: 5 -gcacagggatgaagagaacg-3 , both located in apn intron 3, were used to obtain the full-length sequence of the 871 bp fragment (genbank accession number aj421875). electrophoretic separation and detection were performed on an abi prism 3100 genetic analyzer (perkin elmer, applied biosystems, foster city, ca, usa). pcr products from individuals heterozygous for more than one variation were cloned into the pdrive cloning vector (qiagen pcr cloning kit) using one shot max efficiency dh5␣-t1 competent cells (invitrogen, merelbeke, belgium). plasmids were purified with the qiaprep miniprep spin kit (qiagen, westburg, the netherlands) and checked for inserts by ecori restriction analysis. bidirectional cycle sequencing of plasmids with inserts was performed with the pcr primer set using the abi prism bigdye terminator cycle sequencing ready reaction kit (applied biosystems, foster city, ca, usa). electrophoretic separation and detection were performed on an abi prism 3100 genetic analyzer (perkin elmer, applied biosystems, foster city, ca, usa). a total of 100 healthy unrelated belgian individuals were screened for polymorphisms in the human aminopeptidase n domain that is essential for its hcov-229e receptor activity. an 871 bp fragment, encompassing apn exon 3, intron 3 and exon 4 was pcr-amplified and sequenced, and was submitted to genbank under accession number af527789. the resulting chromatograms were analyzed using the seqman multiple sequence alignment tool (laser-gene, dnastar, madison, wi). consensus sequences were compared with a reference apn sequence in genbank (accession number aj421875) using blast (basic local alignment search tool). 23 seven variations were identified, of which six have not yet been described. table 1 shows the distribution of the allele frequencies. intron variations are described referring to their relative position in the intron, and exon variation positions are referred to their mrna nucleotide position (genbank accession number x13276). the location of the polymorphisms in the apn gene is shown in figure 1 . while no variations could be found in apn exon 3, four of the identified polymorphisms were located in intron 3 and three in exon 4. in intron 3, a c to t variation was found at intron 3 position 86 (c86t) (genbank aj421875, contig position 327) in two individuals, as well as a g to c variation at intron position 395 (g395c) in seven individuals, and a c to t variation at intron position 429 (c429t) in one sample. all individuals were heterozygous for these polymorphisms, which have no apparent functional consequence, as they are located in a non-coding intron region of the apn gene. the fourth observed intron polymorphism, a c to t variation at intron position 389 (c389t) was found in association with three variations in exon 4: an already described c to t polymorphism in codon 311 (genbank x13276, mrna, nt position 956), 24 leading to an alanine to valine substitution, and two silent mutations, a g to t variation in codon 318 (nt 978), and a g to a variation in codon 321 (nt 987). fifteen heterozygotes and one homozygote for these four polymorphisms were found in the group of 100 belgian individuals. in one of these fifteen heterozygous individuals, the intron variation c429t was found. no deviations from expectations under hardy-weinberg assumptions were observed. haplotypes were determined by sequence analysis of cloned pcr-amplicons in samples of individuals heterozygous for more than one variation. five haplotypes were identified, and their frequencies are shown in table 2 . the four linked variations, identified in samples of 16 individuals, were demonstrated to be present on the same allele, and this haplotype was detected with a frequency of 8.5%. in this study we analyzed an 871 bp region of the apn gene, encompassing the full-length apn exon 3, intron 3 and exon 4. in our search for polymorphisms in the apn domain that is essential for its hcov-229e receptor function, we identified seven polymorphisms, of which four were located in the non-coding intron 3. in 25% of the belgian individuals one or more of these seven variations were found. haplotype analysis revealed the presence of five haplotypes in the population. three polymorphisms in apn exon 4 (c956t, g978t and g987a) in association with an intron 3 variation (c389t), were identified at a relatively high allele frequency (8.5%) in our belgian population. fifteen heterozygotes and one homozygote for these four variations were observed. one of the exon 4 single nucleotide polymorphisms is a c to t mutation, c956t, leading to an amino acid change in codon 311. this alanine to valine substitution, a conservative amino acid change, has already been described in a population of italian coeliac disease patients, in which it was observed with an allele frequency of 7.9%. 24 in our population, this polymorphism was approximately equally frequent (8.5%). the c956t polymorphism was always found in combination with the two other observed exon 4 variations (g978t and g987a) and one intron 3 variation (c389t). haploid dna sequencing demonstrated the presence of these four variations on the same allele. here we report for the first time an association between the c956t polymorphism and other variations in the apn gene. absolute linkage between the snps within this short physical distance is commonly observed. apart from the codon 311 variation (c956t), none of the other associated polymorphisms has an apparent functional effect, as the codon 318 and 321 variations (g978t and g987a) are silent, and c389t is located in an intron. recent studies revealed that the human apn gene is subject to alternative splicing, and two splice variants, in which exon 3 and exon 14 were lost, have been identified. 14 alternative splicing is a mechanism that allows different protein isoforms to be created from a single gene. the splicing process is regulated by both cis-and trans-acting factors, which control the choice of 5 or 3 splice sites either positively or negatively. cis-acting regulatory elements include exonic or intronic splice enhancers or silencers, which can be changed by mutations with a possible effect on mrna splicing. 25, 26 in this perspective, the importance of silent mutations or intron variations, which seem to have no apparent functional effect, should be reconsidered. supporting this assumption, a silent mutation (c77g) in exon 4 of the human protein-tyrosine phosphatase cd45 gene has been shown to increase the expression of an aberrant exon 4-included cd45 by disrupting the activity of an exonic splice silencer. an association of this silent mutation with multiple sclerosis has been suggested. 27 in this way, it might be possible that the silent mutations in apn exon 4 and the apn intron 3 variations that we observed in our population could be of functional importance. the alanine to valine substitution in codon 311, caused by the single nucleotide polymorphism c956t, is an amino acid change occurring in the apn domain that is essential for its hcov-229e receptor function. although this amino acid variation is rather conservative, an effect on the hcov-229e binding capacity of aminopeptidase n could be possible. since the three-dimensional structure of apn has not yet been described, molecular modeling studies of the whole protein could not be performed. further research is needed to elucidate the biological relevance of the apn variations described here. in vitro studies should be carried out including in vitro transcription, translation and viral binding assays of the described apn gene variants to detect a possible functional effect. furthermore, a virus susceptibility test can be performed involving healthy volunteers homozygous or heterozygous for these variations. hcov-229e is a relatively innocuous agent and it would be possible to determine whether these polymorphisms could affect susceptibility to infection. given the substantial role of aminopeptidase n in several domains, including disease therapy and diagnosis, studies analyzing the apn gene and the functional consequences of possible gene variations will be of importance in these and future applications. neuroinvasion by human respiratory coronaviruses identification of a novel coronavirus in patients with severe acute respiratory syndrome human aminopeptidase n is a receptor for human coronavirus 229e aminopeptidase n is a major receptor for the entero-pathogenic coronavirus tgev feline aminopeptidase n serves as a receptor for feline, canine, porcine, and human coronaviruses in serogroup i putative hapn receptor binding sites in sars-cov spike protein angiotensin-converting enzyme 2 is a functional receptor for the sars coronavirus analysis of cellular receptors for human coronavirus oc43 structure and expression of aminopeptidase n cd13 (gp150; aminopeptidase-n): predominant functional activity in blood is localized to plasma and is not cell-surface associated molecular cloning, expression, and chromosomal localization of the gene encoding a human myeloid membrane antigen (gp150) human aminopeptidase n is encoded by 20 exons separate promoters control transcription of the human aminopeptidase n gene in myeloid and intestinal epithelial cells single site polymorphisms and alternative splicing of the human cd13 gene -different splicing frequencies among patients with acute myeloid leukaemia and healthy individuals role of alanyl aminopeptidase in growth and function of human t cells (review) aminopeptidase n is a receptor for tumor-homing peptides and a target for inhibiting angiogenesis differential binding of drugs containing the ngr motif to cd13 isoforms in tumor vessels, epithelia, and myeloid cells cd13 (human aminopeptidase n) mediates human cytomegalovirus infection characterization of functional domains in the human coronavirus hcv 229e receptor identification of residues critical for the human coronavirus 229e receptor function of human aminopeptidase n world medical association's declaration of helsinki simple non-invasive method to obtain dna for gene analysis basic local alignment search tool linkage disequilibrium between intra-locus variants in the aminopeptidase n gene and test of their association with coeliac disease misregulation of pre-mrna splicing that causes human diseases. concepts and therapeutic strategies the power of point mutations a cd45 polymorphism associated with multiple sclerosis disrupts an exonic splicing silencer we would like to thank the colleagues of the laboratory of clinical and epidemiological virology, department of microbiology and immunology, rega institute for medical research, university of leuven, belgium, for helpful comments and discussion. this work was supported by a fellowship of the fund for scientific research (fwo), brussels, belgium.conflict of interest: no conflicting interest declared. key: cord-258250-zueo1xfa authors: hirotsu, yosuke; maejima, makoto; shibusawa, masahiro; nagakubo, yuki; hosaka, kazuhiro; amemiya, kenji; sueki, hitomi; hayakawa, miyoko; mochizuki, hitoshi; tsutsui, toshiharu; kakizaki, yumiko; miyashita, yoshihiro; yagi, shintaro; kojima, satoshi; omata, masao title: comparison of automated sars-cov-2 antigen test for covid-19 infection with quantitative rt-pcr using 313 nasopharyngeal swabs including from 7 serially followed patients date: 2020-08-12 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.029 sha: doc_id: 258250 cord_uid: zueo1xfa abstract severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection is determined by reverse-transcription pcr (rt-pcr) in routine clinical practice. in the current pandemic situation, a more rapid and high-throughput method is in growing demand. here, we validated the performance of a new antigen test (lumipulse) based on the chemiluminescence enzyme immunoassay. a total of 313 nasopharyngeal swabs (82 serial samples from 7 infected patients, 231 individual samples from 4 infected patients and 215 non-infected individuals) were analyzed for sars-cov-2 by quantitative rt-pcr (rt-qpcr) and then subjected to lumipulse. we determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the antigen test performance with that of rt-qpcr. further, we compared the viral loads and antigen levels in serial samples from seven infected patients. when using rt-qpcr as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity with a 91.4% overall agreement rate (286/313). in specimens with > 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with rt-qpcr, respectively. this concordance declined with lower viral loads. in the serially followed patients, the antigen levels showed a steady decline along with viral clearance. this gradual decline was in contrast with the abrupt “positive-to-negative” and “negative-to-positive” status changes observed with rt-qpcr, particularly in the late phase of infection. in summary, the lumipulse antigen test can rapidly identify sars-cov-2-infected individuals with moderate to high viral loads and may be helpful for monitoring viral clearance in hospitalized patients. in the current pandemic situation, a more rapid and high-throughput method is in growing demand. here, we validated the performance of a new antigen test were analyzed for sars-cov-2 by quantitative rt-pcr (rt-qpcr) and then subjected to lumipulse. we determined the cutoff value for antigen detection using receiver operating characteristic curve analysis and compared the antigen test performance with that of rt-qpcr. further, we compared the viral loads and antigen levels in serial samples from seven infected patients. when using rt-qpcr as the reference, the antigen test exhibited 55.2% sensitivity and 99.6% specificity with a 91.4% overall agreement rate (286/313). in specimens with > 100 viral copies and between 10 and 100 copies, the antigen test showed 100% and 85% concordance with rt-qpcr, respectively. this concordance declined with lower viral loads. in the serially followed patients, the antigen levels showed a steady decline along with viral clearance. this gradual decline was in contrast with the abrupt "positive-to-negative" and "negative-to-positive" status changes observed with rt-qpcr, particularly in the late phase of infection. in summary, within a few months, sars-cov-2 had spread around the world, threatening human life [2] . to date, 11 million individuals have been infected with sars-cov-2 and 0.52 million patients have died from coronavirus disease 2019 (covid-19) [2] . as japan continues to battle the covid-19 epidemic with a second wave, more than one thousand newly infected patients have been confirmed daily. in japan, 38,687 individuals were infected with sars-cov-2 and 1,012 patients passed away by 3th, august, 2020. j o u r n a l p r e -p r o o f 5 the world health organization (who) has raised a global warning and announced the need for a test system for covid-19-suspected patients [3] . sars-cov-2 is now known to also be spread by infected people who experience only mild symptoms or are asymptomatic carriers [4] [5] [6] . therefore, there is a need to expand testing to asymptomatic individuals depending on the regional situation. furthermore, there are concerns that environmental contamination is resulting in further spread of the virus, particularly in hospitals [7, 8] . in routine clinical practice, sars-cov-2 infection is determined by reverse-transcription pcr (rt-pcr) analysis [9] . the rt-pcr test is conducted using different types of specimens including sputum, nasopharyngeal swabs, pharyngeal swabs, saliva, stool, bronchoalveolar lavage fluid, and endotracheal aspirate fluid [10] [11] [12] . as we and other group previously reported, using a pooling strategy with rt-pcr is one of the most effective methods for screening individuals, realizing savings in terms of time, reagents, and cost [13, 14] . however, the rt-pcr test is not rapid (it typically takes 3-4 h), and it requires specialized laboratory equipment and skilled technicians, while antigen j o u r n a l p r e -p r o o f tests are a simple method that can be performed routinely in clinical laboratories [15, 16] . antigen tests have been widely applied to detect infection with viruses other than sars-cov-2 [16] . therefore, the development of a more costeffective and high-throughput test system is important for preventing viral spread and monitoring the level of infection in covid-19 patients. here, we present a newly developed sars-cov-2 antigen test system based on the chemiluminescence enzyme immunoassay (cleia). we compared the quantitative rt-pcr (rt-qpcr) results for viral load with the cleia results for antigen level following testing of 313 nasopharyngeal swabs. moreover, we examined the antigen levels in a series of samples collected from hospitalized patients with covid-19 infection. we collected 313 nasopharyngeal swabs from individuals at yamanashi central hospital. all samples were obtained using cotton swabs and viral transport media in utm® (copan diagnostics, murrieta, ca, usa). the viral j o u r n a l p r e -p r o o f transport media were stored at 4°c until nucleic acids extraction. total nucleic acids were extracted within 2 hours after swab collecting. (thermo fisher scientific) as previously described [14, 17] . briefly, we added 200 µl of viral transport media, 5 µl of proteinase k, 265 μl binding solution, 10 μl total nucleic acid-binding beads, 0.5 ml wash buffer, and 0.5-1 ml of 80% ethanol to each well of a deep-well 96-well plate. nucleic acids were eluted with 70 μl elution solution. total nucleic acids were immediately subjected to the following rt-qpcr test and residual samples were stored at −80°c. according to the protocol developed by the national institute of infectious diseases (niid) in japan [18] , we performed one-step rt-qpcr to detect sars-cov-2 [19] . a threshold cycle (ct) value was assigned to each pcr reaction and the amplification curve was visually assessed. according to the national protocol (version 2.9.1), we deemed a sample to be positive when a visible amplification plot was observed, whereas a sample was deemed negative when no amplification was observed. the absolute copy number of the viral load was determined using the ct value of the accuplex sars-cov-2 reference (seracare, milford, ma, usa). the remaining viral transport media from each nasopharyngeal swab was frozen after rt-qpcr. these samples were sent to an outside laboratory (fujirebio, inc., tokyo, japan). once thawed, the viral transport medium was viscous; hence, samples were centrifuged at 1,300 ×g for 10 min and the supernatants were used for subsequent analysis. we used 100 µl of the supernatant per sample of thawed viral transport media from each nasopharyngeal swab to measure the antigen level with the lumipulse sars-cov-2 ag kit (fujirebio) on the lumipulse g600ii automated immunoassay analyzer (fujirebio) based on the cleia method. in this assay, the treatment solution and the sample were consecutively aspirated using a single tip. the mixture was dispensed into the anti-sars-cov-2 ag monoclonal antibody-coated magnetic particle solution and then incubated for 10 minutes at 37°c. after the first wash step, alkaline phosphatase-conjugated anti-sars-cov-2 ag monoclonal antibody was then added and incubated for 10 minutes at 37°c. after another wash step, the substrate solution was added and incubated for 5 minutes at 37°c. the when the antigen level could not be measured because it exceeded the detection limit, we tested diluted samples and calculated the antigen level of the original sample based on the dilution factor. statistical analysis was performed in r (https://www.r-project.org/) and excel (microsoft corp., redmond, wa, usa). receiver operating characteristic (roc) curve analysis was conducted using analyse-it (analyse-it software, ltd., leeds, uk) to evaluate the assay performance and to visualize the curves. areas under the roc curves, sensitivity, and specificity were calculated. the median antigen level of the pcr-positive samples was 1.57 pg/ml (range 0.12-194,795 pg/ml) and that of the pcr-negative samples was 0.27 pg/ml (range 0-2.46 pg/ml) (fig. 1a) . the mean antigen level of the pcrpositive samples was significantly higher than that of the pcr-negative samples (p = 0.02, student's t-test, fig. 1a ). to determine the cutoff antigen level for distinguishing sars-cov-2 infection status, we conducted roc curve analysis. when the cutoff for the antigen level was set to 1.31 pg/ml, the accuracy reached its highest level. roc analysis yielded an area under the roc curve (auc) value of 0.848 ± 0.044, suggesting the antigen test accurately detected sars-cov-2 (fig. 1b) . the numbers of true-positive, false-positive, true-negative, and false-negative results were 32, 1, 254, and 26, respectively (fig. 1c) . when the rt-qpcr results were used as a reference, the antigen test diagnosed sars-cov-2 infection status with a sensitivity of 55.2% and a specificity of 99.6%. the overall concordance between rt-qpcr and the antigen test was 91.4% (286/313). the primer/probe set used in rt-qpcr amplified the nucleocapsid gene of sars-co-v-2 [19] . the antigen test also detects a portion of the nucleocapsid protein. we next examined the relationship between the sars-cov-2 viral loads (as determined by rt-qpcr) and the antigen levels (fig 2) . the sars-cov-2 viral load was positively correlated with the antigen level (r² = 0.768). to examine the reason underlying the low sensitivity of the antigen test, we investigated the relationship between the number of viral copies in the samples and the positive results obtained with the antigen test. the antigen test determined samples to be positive with 100% concordance with rt-qpcr when the viral load in the samples was > 100 copies (17/17 samples) and 85% concordance when the viral load was > 10 copies but < 100 copies (23/27 samples) ( table 1 ). the concordance rate gradually declined with decreasing viral load (60% concordance for samples with 10-100 copies, 33% for samples with 1-10 copies, and 26% for samples with less than 1 copy; table 1 ). therefore, the antigen test was highly accurate when the viral load was j o u r n a l p r e -p r o o f > 100 copies, whereas lower viral loads (< 100 copies) resulted in some samples being missed (i.e., false-negative results). we performed the antigen test and rt-qpcr on a series of nasopharyngeal swabs from seven infected patients. a total of 82 samples were collected from these patients (range 5-27 samples per patient). overall, there was a strong correlation between the rt-qpcr and antigen test results (fig. 3) . during the clinical course of these seven patients, the antigen levels showed a similar declining trend along with viral load as quantitated by rt-qpcr (fig. 3) . of particular interest, there were abrupt positive-to-negative turns and negative-to-positive turns based observed with rt-qpcr, especially when the viral load decreased in the latter phase of the infection (cases #2 and #3, fig. 3 ), whereas the antigen test rarely showed these abrupt "turns". in this study, we validated the assay performance of an antigen test based on cleia (lumipulse) and compared the results with rt-qpcr. to our knowledge, this is the first report on the clinical validation of the lumipulse sars-cov-2 ag kit. this antigen test is commercially supplied by fujirebio, inc. (tokyo, japan) and it was recently approved as an in vitro diagnostic test for covid-19 on june 19, 2020, in japan. compared with the rt-qpcr test, this antigen test can process 60-120 samples in 30 min per run on an automated machine, which greatly shortens the turnaround time. this test could, therefore, be used as a routine high-throughput test in a hospital setting, especially during a pandemic situation. there are some limitations of the antigen test. the antigen test has low sensitivity compared with rt-qpcr being able to detect a lower sars-cov-2 titer by means of the pcr amplification process. however, the antigen test accurately detected sars-cov-2 in all samples with > 100 copies/test. where samples had a viral load of < 100 copies as quantitated by rt-qpcr, the sensitivity of the antigen test decreased. second, the presence of sars-cov-2 antigen does not necessarily mean the presence of viable virus. we should carefully consider whether sars-cov-2 antigen-positive patient is infectious to other persons. the viral load tended to be higher at the onset of infection, which is when human-to-human transmission is at its highest [20, 21] . epidemiologically, one of the key issues is finding asymptomatic and presymptomatic "super spreaders" to prevent community and nosocomial infection [22] . super spreaders are more likely to be high viral load carriers. along with viral loads, super spreader would go out with a lot of contact, be close distance with other people and talk loudly without waring mask. the clusters of covid-19 were reported at closed environments, which would contribute to secondary transmission and promote super-spreading events [23] . in this context, our results revealed that the antigen test could be used to identify covid-19-infected individuals who pose a high risk of transmission. according to the guidelines of the japanese government, saliva, as well as nasopharyngeal swabs, can be used for testing with the lumipulse sars-cov-2 ag kit. notably, the self-collection of saliva may decrease the infection risk of healthcare workers [11] . the japanese government recommends that the antigen test and nucleic acid amplification test of saliva be applied to symptomatic patients within 9 days of onset when viral loads are high. in the usa, the sofia sars antigen fluorescent immunoassay (fia) notably, our results for seven patients who were followed from the time of admission to that of hospital discharge suggested that the sars-cov-2 antigen levels declined in these consecutively collected samples. this implied that antigen levels could be used to distinguish between the early and late phases of the covid-19 clinical course. the stable trend in the serial antigen test results contrasted with the abrupt changes observed when using rt-qpcr, which often showed mixed "negative" and "positive" results for the same sample. this may confuse clinicians when they wish to investigate treatment effects or the timing of discharge, for example. thus, the lumipulse antigen test may offer a wide in summary, both rt-qpcr and lumipulse antigen test quantitatively measure virus rna and antigen level, respectively. therefore, we could investigate monitor the clinical condition of covid-19 patients using these tests. furthermore, both tests are expected to identify the asymptomatic or presymptomatic sars-cov-2 infected persons who are likely to have high viral loads. combination assay will help us to estimate the infection phase of covid-19 patients in routine clinical practice. and all of the medical and ancillary hospital staff and the patients for consenting to participate. we thank natasha beeton-kempen, ph.d., from edanz group (https://en-author-services.edanzgroup.com/) for editing a draft of this manuscript. yh reports receiving grant support from fujirebio; sy and sk, being employed by fujirebio. no other potential conflict of interest relevant to this article was reported. yh contributed to study design, data collection, data analysis and writingreview (c) comparison of data obtained with the ag test and rt-qpcr. an overall agreement of 91.4% was achieved between the two tests, with 55.2% sensitivity and 99.6% specificity obtained with the ag test. a positive correlation (r² = 0.768) was observed between the sars-cov-2 antigen (ag) level (log10 pg/ml) and the viral titer (log10 copies/test). j o u r n a l p r e -p r o o f a novel coronavirus from patients with pneumonia in china organization wh: coronavirus disease (covid-19) situation reports world health organization, laboratory testing for coronavirus disease (covid-19) in suspected human cases substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (sars-cov2) presumed asymptomatic carrier transmission of covid-19 transmission of 2019-ncov infection from an asymptomatic contact in germany air, surface effective for the eradication of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) in contaminated hospital rooms: a patient from the diamond princess cruise ship detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study. the lancet infectious diseases consistent detection of 2019 novel coronavirus in saliva detection of sars-cov-2 in different types of clinical specimens sample pooling as a strategy to detect community transmission of sars-cov-2 pooling rt-pcr test of sars-cov-2 for large cohort of 'healthy' and infection-suspected patients: a prospective and consecutive study on 1,000 individuals in vitro diagnostics of coronavirus disease 2019: technologies and application routine use of point-of-care tests: usefulness and application in clinical microbiology analysis of covid-19 and non-covid-19 viruses, including influenza viruses, to determine the influence of intensive preventive measures in japan development of genetic diagnostic methods for novel coronavirus 2019 (ncov-2019) in japan double-quencher probes improve detection sensitivity toward severe acute respiratory syndrome coronavirus 2 (sars-cov-2) in a reverse-transcription polymerase chain reaction (rt-pcr) assay virological assessment of hospitalized patients with covid-2019 temporal dynamics in viral shedding and transmissibility of covid-19 asymptomatic and presymptomatic transmission of sars-cov-2: a systematic review closed environments facilitate secondary transmission of coronavirus disease 2019 (covid-19) this study was supported by a grant-in-aid for the genome research project from yamanashi prefecture (to m.o. and y.h.), the japan society for the the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-297396-r1p7xn3a authors: ng, ming-yen; wan, eric yuk fai; wong, ho yuen frank; leung, siu ting; lee, jonan chun yin; chin, thomas wing-yan; lo, christine shing yen; lui, macy mei-sze; chan, edward hung tat; fong, ambrose ho-tung; yung, fung sau; ching, on hang; chiu, keith wan-hang; chung, tom wai hin; vardhanbhuti, varut; lam, hiu yin sonia; to, kelvin kai wang; chiu, jeffrey long fung; lam, tina poy wing; khong, pek lan; liu, raymond wai to; man chan, johnny wai; ka lun alan, wu; lung, kwok-cheung; hung, ivan fan ngai; lau, chak sing; kuo, michael d.; ip, mary sau-man title: development and validation of risk prediction models for covid-19 positivity in a hospital setting date: 2020-09-15 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.022 sha: doc_id: 297396 cord_uid: r1p7xn3a objectives: to develop:(1) two validated risk prediction models for covid-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. methods: patients with and without covid-19 were included from 4 hong kong hospitals. database was randomly split 2:1 for model development database (n = 895) and validation database (n = 435). multivariable logistic regression was utilised for model creation and validated with the hosmer-lemeshow (h-l) test and calibration plot. nomograms and probabilities set at 0.1, 0.2, 0.4, 0.6 were calculated to determine sensitivity, specificity, positive predictive value (ppv) and negative predictive value (npv). results: 1330 patients (mean age 58.2 ± 24.5 years; 50.7% males; 296 covid-19 positive) were recruited. first prediction model developed had age, total white blood cell count, chest x-ray appearances and contact history as significant predictors (auc = 0.911 [ci = 0.880-0.941]). second model developed has same variables except contact history (auc = 0.880 [ci = 0.844-0.916]). both were externally validated on h-l test (p = 0.781 and 0.155 respectively) and calibration plot. models were converted to nomograms. lower probabilities give higher sensitivity and npv; higher probabilities give higher specificity and ppv. conclusion: two simple-to-use validated nomograms were developed with excellent aucs based on readily available parameters and can be considered for clinical utilisation.  developed two simple-to use nomograms for identifying covid-19 positive patients  probabilities are provided to allow healthcare leaders to decide suitable cut-offs  variables are age, white cell count, chest x-ray appearances and contact history  model variables are easily available in the general hospital setting. objectives: to develop: (1) two validated risk prediction models for covid-19 positivity using readily available parameters in a general hospital setting; (2) nomograms and probabilities to allow clinical utilisation. patients with and without covid-19 were included from 4 hong kong hospitals. database was randomly split 2:1 for model development database (n=895) and validation database j o u r n a l p r e -p r o o f calibration plot. models were converted to nomograms. lower probabilities give higher sensitivity and npv; higher probabilities give higher specificity and ppv. two simple-to-use validated nomograms were developed with excellent aucs based on readily available parameters and can be considered for clinical utilisation. coronavirus disease 2019 has spread rapidly worldwide and as of 6 th september 2020, there are now ~27 million cases worldwide and ~900,000 deaths 1 . respiratory and non-respiratory complications of covid-19 are also becoming increasingly apparent 2, 3 . reverse transcription polymerase chain reaction (rt-pcr) is regarded as a vital tool in identifying the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and quarantining covid-19 patients to prevent further spread of the disease 4 . furthermore, it is the definitive test in confirming the diagnosis of covid-19. however, availability of rt-pcr kits maybe difficult in various countries 4 and from specimen collection to report generation, the tests could take 48-72 hours to confirm a positive or negative result 5 . therefore, clinical assessment, blood tests and imaging have been recommended to help identify potential covid-19 positive patients 6 . various strategies have been proposed including widespread computed tomography (ct) scanning 7-9 , greater use of chest x-rays (cxr) 10, 11 , identification of low lymphocyte counts 8, 11 to determine patients more likely to have covid-19 12, 13 and thus more suitable for testing. as yet, the data which supports these strategies are predominantly based on data of covid-19 patients 12, 13 but without comparisons to patients with other conditions and symptoms overlapping with covid-19 (eg. fever, shortness of breath, cough). several issues have arisen in trying to determine the likelihood of a covid-19 diagnosis. firstly, in the early stages of the pandemic when the disease was limited to a few countries, travel and contact history may have been helpful to increase suspicion of a covid-19 j o u r n a l p r e -p r o o f diagnosis, but in some countries where there is established community transmission, this has resulted in patients being covid-19 positive but with no knowledge of possible contact. secondly, different countries have adopted different strategies due to socioeconomic factors and healthcare resources. thus, a covid-19 prediction model based on clinical, laboratory and radiological findings which presents the sensitivity, specificity, positive predictive value (ppv) and negative predictive value (npv) would allow public healthcare systems to decide a suitable strategy on prioritizing tests when such rt-pcr availability is constrained. in this study, we aimed to construct a prediction model utilising patient characteristics, commonly available hematological and biochemical blood tests and cxr findings which can identify covid-19 patients within a cohort of patients who presented to hospitals for various disease conditions and underwent testing for covid-19. in addition, we aimed to create a separate model in the event that contact history is not available in order to determine the presence of covid-19. research ethics approval was obtained from the hong kong west cluster cxr images were searched via the electronic patient record system. baseline cxr images were reviewed and interpreted by radiologists blinded to the patient's covid-19 status. assessment was based on identifying the common findings of covid-19 on cxr which were (i) consolidation or ground glass opacity and (ii) absence of pleural effusion 14, 17 . this was done in a binary format (present or absent) to make this more reproducible in the clinical environment for front-line clinicians. image quality was assessed in 702 randomly chosen cxrs (53% of entire cohort of cxrs) by 8 radiologists separately. we ensured that the cxrs were taken from each of the 4 hospitals. image quality was assessed on a scale from 1 to 3. see supplementary table 2 for examples of cxrs graded as 1, 2 and 3. briefly, cxrs which could not be interpreted with any confidence were graded 1. cxrs with suboptimal image quality but lung changes and pleural effusion could be interpreted with some confidence were graded 2. cxrs with good quality such that lung changes and pleural effusions can be diagnosed with high confidence were graded 3. patients positive for covid-19 were compared to those negative for covid-19 patients. continuous variables were compared using student t-tests. categorical variables were compared using chi-squared tests. the database was randomly split on a 2:1 basis for the the selection was finished until the difference in bic of all remaining risk factors <10. 18 to test the nonlinear effect of selected clinical parameters, quadratic term of significant continuous predictors were considered. given that patients can present without knowledge of contact history with an infected person, a further model was developed with one having contact history removed, to represent an event in which contact history is unknown. in order to validate the model, the discrimination and calibration power of models were examined. the area under the receiver operating characteristic curve (auc) were conducted to evaluate the discrimination power, where 0.7 to 0.8 of auc is considered acceptable, 0.8 j o u r n a l p r e -p r o o f to 0.9 is considered excellent, and more than 0.9 is considered outstanding discrimination power. meanwhile, hosmer-lemeshow (h-l) test and calibration plot was used to test how well the percentage of observed covid-19 positive matches the percentage of predicted covid-19 positive over deciles of predicted risk. a p-value >0.05 is needed to conclude that there are insignificant differences between the observed and expected outcomes and therefore the model has good overall calibration. different probabilities were used to evaluate the model performance based on the sensitivity, specificity, ppv and npv. sensitivity analysis was conducted to examine the robustness of the model. multiple imputation was applied to handle missing data. the chained equation method was used to impute each missing value twenty times, adjusted for all baseline covariates and outcomes. moreover, 10-fold cross validation was applied to evaluate the discrimination and calibration power. to facilitate the risk prediction models used for screening in routine busy clinical practice, simple nomograms were developed. the effect of each predictor in the model was converted to a score and summation of all predictors that can be mapped to an estimated risk of covid-19 positive. the nomograms were plotted using nomolog package in stata 19 . sensitivity, specificity, ppv, npv were determined for the following probabilities which were: figure 3 and figure 4 were developed based on the derived risk prediction models. using the overall cohort model nomogram (figure 3 ) as an example, if a patient suspected to have covid-19 is aged 50, has no contact history, wcc of 2x10 9 cells/l and a cxr with no consolidation/ggo and absent pleural effusion (peff) the scoring will be as follows: age has two steps, so for age 50 at step 1, allocate 2 points; for step 2: allocate 7.5 points. for no contact history which is step 3, allocate 0 points. for a total white cell count (wcc) of 2x10 9 cells/l at step 4: allocate 7 points. for a cxr with no consolidation/ggo and absent peff at step 5, allocate 0 points. therefore, they would be allocated a total score of 16.5 points which equates to 0.6-0.7 probability (ie. 60-70% probability) of being covid-19 positive. in our study, we have developed two risk prediction models for determining covid-19 positive patients which have been validated with a separate dataset. both models have an excellent auc with good matching with the validation dataset. the models are based on parameters (ie. total wcc, cxr consolidation/ggo with absent pleural effusions) which are available in general hospitals as well as clinical data (ie. age with or without contact history). we have also provided nomograms to determine probability of covid-19 with several different probabilities illustrated to show the sensitivity, specificity, ppv and npv so that clinicians or healthcare systems can decide which probabilities would make the best cut-offs for rt-pcr testing. the development of these nomograms will hopefully improve frontline clinicians' diagnostic accuracy in identifying patients with covid-19 where rt-pcr may not be available or rapid results cannot be provided. commission. thus our data provides evidence that these initial observations of covid-19 were indeed accurate. cxr consolidation/ggo with absent pleural effusions is the typical appearance of covid-19 radiologically 14 . this model confirms that using cxr in addition to other parameters is j o u r n a l p r e -p r o o f helpful in identifying covid-19 patients. this has already been incorporated into societal recommendations and our models provide evidence to support this approach despite the lower sensitivity of cxr compared to ct 10, 11 . our model did not incorporate ct as ct was not easily available for our covid-19 positive patients and indeed the negative patients. this would likely be the scenario globally during this pandemic. ct with its higher sensitivity 21 will likely improve diagnostic accuracy but this is dependent on the facilities in each health service. not all health services can dedicate ct scanners for covid-19 diagnosis due to either a lack of scanner availability and/ or the extensive cleaning required after each covid-19 scan which reduces the radiology department's productivity 22 . in our study, we wanted to focus on parameters which would be easily accessible to all patients seen in the general hospitals, as some health systems even struggle to make chest x-rays and wcc available 23 . in our cohort, age is a significant predictor for covid-19. in this, study, the covid-19 patients were significantly younger than the negative patients. this can be partly explained by younger patients being more mobile and thus being more susceptible to develop covid-19 compared to the older population who may travel less. review of previous publications have indicated that patients with covid-19 are usually younger. in korea, one paper indicated that >60% of patients 24 were <49 years old whilst in china, 51.2%-55.1% 12, 13 of patients were <49 years old. the two nomograms in this study allocated higher scoring to the younger patients including children. this is possibly due to children having less symptoms and even less radiological changes 25, 26 making the identification of covid-19 more difficult. indeed, this possibly explains the noticeably less children confirmed to have covid-19 and possibly explains the statistical significance of age in the models for determining patients who are positive for sars-cov2. however, age as a predictor is very much representative of this cohort. in a different healthcare system where more elderly patients present, age as a predictor will likely need to be further investigated. the models we have established can set different probabilities in order to allow medical systems to self-determine the pre-test probability required for rt-pcr testing. moreover, the nomograms have been developed to visualize the sophisticated mathematical equation so that it can be adopted in the routine busy clinical practice. however, it should be emphasised that rt-pcr remains the gold standard for diagnosing covid-19 and that focus should be made on making rt-pcr easily available for testing patients as well as increasing the time taken for results to be made available. our study has several limitations. firstly, the covid-19 cases are reflective of practice in hong kong which has been active in screening for covid-19 which has included asymptomatic patients (5.6% in this cohort) with contact history and patients with mild symptoms. this may not be representative in other health systems worldwide so this model needs to be validated in those health systems. secondly, the chest x-rays were assessed by radiologists, so whether these results will be similar with frontline clinicians is uncertain. however, the assessment was simplified in order that frontline clinicians can focus their search on cxr to consolidation/ggo and absence of pleural effusions. furthermore, some health systems have access to radiology support to review cxrs and this model possibly justifies this practice if logistically feasible. thirdly, inflammatory markers like c-reactive protein, creatnine kinase, lactacte deyhydrogenase were not included in the model as a significant proportion of patients did not have these markers measured at time of admission. whether these markers prove useful will require further study. lastly, asymptomatic patients made up a very small proportion of patients and thus further validation with an asymptomatic cohort would be required to validate this model. in conclusion, we present two models which have 3 or 4 readily available parameters to improve the accuracy of identifying covid-19 amongst patients suspected of having covid-19 with or without known contact history. this will help identify patients most likely to benefit from rt-pcr testing and thus help better allocate rt-pcr testing where this resource is limited. table 2 . a total score is calculated from the addition of the scores for the variables chest x-ray (cxr) consolidation/ ground glass opacity (ggo), contact history, white cell count and age. note that age has two steps whilst other variables only have 1 step. the total score can then be marked on the bottom row and compared with the probability scale above. for example, a patient suspected to have covid-19 aged 50 (step 1: allocate 2 points; step 2: allocate 7.5 points), has no contact history (step 3: allocate 0 points), total white cell count (wcc) of 2x10 9 cells/l (step 4: allocate 7 points) and a cxr with no consolidation/ggo and absent pleural effusion (pe) (step 5: allocated 0 points), would receive a total score of 16.5 points which equates to a probability of between 0.6 and 0.7. a clinician then refers to the probability table (table 3) and decides what degree of sensitivity, specificity, positive predictive value or negative predictive value is adequate for their setting. table 4 . a total score is calculated from the addition of the scores for the variables pleural effusion, chest x-ray (cxr) consolidation/ ground glass opacity (ggo), white cell count, age and vomiting symptom. note that age has two steps whilst other variables only have 1 step. the total score can then be marked on the bottom row and compared with the probability scale above. for example, a patient suspected to have covid-19 aged 40 (step 1: allocate 2 points; step 2: allocate 8.5 points), total white cell count (wcc) of 8x10 9 cells/l (step 3: allocate 3 points) and a cxr with consolidation/ggo and absent pleural effusion (pe) (step 4: allocated 1.5 points), would receive a total score of 15 points which equates to a probability of between 0.6 and 0.7. a clinician then refers to the probability table (table 3) and decides what degree of sensitivity, specificity, positive predictive value or negative predictive value is adequate for their setting. world health organization. coronavirus disease (covid-19) weekly epidemiological update recovered covid-19 patients show ongoing subclinical myocarditis as revealed by cardiac magnetic resonance imaging world health organization. laboratory testing strategy recommendations for covid-19 guidance and standard operating procedure covid-19 virus testing in nhs laboratories the role of chest imaging in patient management during the covid-19 pandemic: a multinational consensus statement from the fleischner society covid-19): a perspective from china therapeutic and triage strategies for 2019 novel coronavirus disease in fever clinics covid-19 pneumonia: what has ct taught us? the lancet infectious diseases acr recommendations for the use of chest radiography and computed tomography (ct) for suspected covid-19 infection british society of thoracic imaging. bsti nhse covid-19 radiology decision support tool clinical features of patients infected with 2019 novel coronavirus in wuhan, china. the lancet 2020;0:201160. 15. world health organization. global surveillance for covid-19 caused by human infection with covid-19 virus: interim guidance improved molecular diagnosis of covid-19 by the novel, highly sensitive and specific covid-19-rdrp/hel real-time reverse transcription-polymerase chain reaction assay validated <em>in vitro</em> and with clinical specimens imaging profile of the covid-19 infection: radiologic findings and literature review bayesian model selection in social research design and evaluation of analytical tools for emergency department management based on machine learning techniques index for rating diagnostic tests sensitivity of chest ct for covid-19: comparison to rt-pcr a role for ct in covid-19? what data really tell us so far adoption of covid-19 triage strategies for low-income settings transmission potential and severity of covid-19 in south korea clinical and epidemiological features of 36 children with coronavirus disease 2019 (covid-19) in zhejiang, china: an observational cohort study. the lancet infectious diseases differences in clinical and imaging presentation of pediatric patients with covid-19 in comparison with adults sensitivity, specificity, positive predictive value and negative predictive value are stated in percentage with 95% confidence intervals in brackets key: cord-301079-n1nytr6k authors: tan, li; ma, boyi; lai, xiaoquan; han, lefei; cao, peihua; zhang, junji; fu, jianguo; zhou, qian; wei, shiqing; wang, zhenling; peng, weijun; yang, lin; zhang, xinping title: air and surface contamination by sars-cov-2 virus in a tertiary hospital in wuhan, china date: 2020-07-27 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.027 sha: doc_id: 301079 cord_uid: n1nytr6k abstract background few studies have explored the air and surface contamination by sars-cov-2 virus in healthcare settings. methods we collected air and surface samples from the isolation wards and intensive care units designated for covid-19 patients. the clinical data and tests result of nasopharyngeal specimens and serum antibodies were also collected from the sampling patients. results a total of 367 air and surface swabbing samples were collected from the patient care areas of 15 mild and 9 severe/critical covid-19 patients. only one air sample taken during the intubation procedure tested positive. high-touch surfaces were slightly more likely contaminated by the rna of the sars-cov-2 virus than low-touch surfaces. contamination rates was slightly higher near severe/critical patients compared to those near mild patients, although not statistically significant (p <0.05). surface contamination was still found near the patients with both positive igg and igm. conclusions air and surface contamination of the viral rna was relatively low in healthcare settings after enhancement of infection prevention and control. environmental contamination could still be found near seroconverted patients, suggesting the needs of maintaining constant vigilance in healthcare settings to reduce healthcare associated infection during the covid-19 pandemic. since its first emergence in december 2019 in wuhan city, china, the novel coronavirus sars-cov-2, has spread to over 200 countries and regions within five months (phelan et al., 2020) . as of 30 june 2020, the total cases of covid-19 infection have reached over 10 million globally, and the death toll were nearly 500,000 (2020). similar to two previous coronaviruses, sars-cov (ip et al., 2004) and mers-cov (hunter et al., 2016) , this newly emerged virus has caused outbreaks in healthcare settings (chan et al., 2020) . the fast spread of covid-19 infection j o u r n a l p r e -p r o o f could have been facilitated by transmission of mild, pre-symptomatic and even asymptomatic cases (kam et al., 2020 , rothe et al., 2020 , suggesting that early detection of cases might be a challenge in healthcare settings. studies have shown that viral shedding could peak soon after symptom onset (wölfel et al., 2020) , and viral loads of asymptomatic covid-19 patients could be as high as those of symptomatic cases (zou et al., 2020) . similar to sars-cov, the aerosols of novel coronavirus sars-cov-2 could survive in air up to three hours, on plastic and stainless steel surfaces up to 72 hours in a controlled experimental environment (van doremalen et al., 2020) . the rna of sars-cov-2 has been detected in respiratory specimens, faeces, blood, and urine samples , young et al., 2020 . previous studies have reported that viral shedding of sars-cov-2 peaked soon after symptom onset, and peaked within one week (wolfel et al., 2020) . most patients were seroconverted within two weeks, and seropositivity of igg appeared slightly earlier than those of igm . the current evidence suggests that serum antibody levels might not be associated with disease severity, but it remains unclear whether viral shedding could be lower among those with both elevated igm and igg . here we collected air and surface samples from isolation wards and icu units of a tertiary hospital in wuhan, with the aim to evaluate environmental contamination after enhancement of infection prevention and control measures (ipc) during the covid-19 pandemic. we also assess the association of patients' disease severity, seroconversion status and environmental contamination. j o u r n a l p r e -p r o o f the whole hospital areas were classified into low-and high-risk areas with different ipc measures implemented. the latter included triage stations, fever clinics, outpatient clinics and wards of respiratory and infectious diseases, and emergency department. the rest were classified as low-risk areas. hcp including doctors, nurses, and ward assistants were required to put on a full set of personal protective equipment (ppe) when working in highrisk areas, whereas only surgical masks were required for those working in low-risk areas. the detailed requirement for ppe can be found in supplementary table 1 there was no airborne infection isolation rooms (aiir) in this hospital. to reduce the risk of airborne transmission, the central air conditioning system was turned off and natural ventilation was used in isolated wards. windows were kept open for 30min at least twice per day, and one electronic fan was installed on the top of windows in each inpatient ward to increase ventilation. if there was no patients inside the room, ultraviolet lights (wavelength 253.7 nm, shuangsheng medical ltd, sx-01a) were used to disinfect empty isolation rooms for at least one hour. in clean areas (green zone in supplementary figure 1 ), it was followed by 3% hydrogen peroxide spray and closed for two hours' disinfection. surfaces of premises and floors were disinfected twice per day using sodium hypochlorite at 1000mg/l. in the incident of spillage, sodium hypochlorite at 5000mg/l was used to disinfect soiled premise or floor. in the event of large spillage by blood, vomits and other body fluids, soiled premise or floor were immediately covered by sodium hypochlorite at 5000mg/l for 30min followed by disinfection of sodium hypochlorite at 1000mg/l. during 14 -29 march 2020, the ipc team of the ovb hospital conducted a comprehensive investigation on environmental contamination of sars-cov-2 virus. selection of patients in our study was subject to the consent given by patients, and availability of manpower. to investigate the contamination risks of aerosol generating procedure, we particularly selected at least one patient who was receiving one of the following ways of oxygen therapy at the time of sampling: oxygen supply via nasal cannula, invasive ventilation via tracheostomy, invasive ventilation via endotracheal intubation, and ecmo. additional j o u r n a l p r e -p r o o f numbers of mild and severe patients were then recruited from different patient rooms given the availability of manpower and testing kits. a total of 24 patients, 15 in the general isolation wards and 9 in the icu, were selected from eleven wards given the availability of manpower and testing kits. the anonymized demographic and clinical data of these patients were collected from the electronic medical records of the ovb hospital. in the general isolation wards, three patients stayed in one room and were advised not to walk around except going to bathroom. most severe/critical patients stayed in single rooms in the intensive care unit (icu). the individual patient data and a floor plan of sampling sites in the icu can be found in supplementary file. surface samples were taken from before daily decontamination procedures. experienced infection control nurses who wore full ppe swabbed selected high-touch surfaces, including patients' mobile phones, bedrails, door handles, light switches, side tables, and medical instruments in patient wards, as well as low-touch surfaces including floors, chairs in the corridor. surface sampling was conducted before the routine clean procedure. each surface was sampled by two pre-moistened sterile cotton swabs simultaneously, both were immediately put into one tube of viral transport media (vtm, yocon ltd, beijing, china). air samples were taken by placing an air sampler within one meter of patient head, which continuously filtered air and trapped small virus particles by a membrane at the speed of 5l/min. after one hour the membrane was removed and cut into small pieces to be stored in vtm for further tests. the air sampler was placed at the same height of (or slightly lower than) an electronic fan installed on top of windows to expel the air from wards to outside. air samples were taken from patient rooms, the corridor outside patient room, and nearby nurse stations. hand swabs were collected from both hands of mild patients. we did not swab the hands of severe and critical patients due to their conditions. the outer and inner layer of surgical masks worn by these patients was cut into small pieces that were immediately kept in vtm for laboratory tests. the body fluid samples of sputum and alveolar lavage fluids were also taken from some severe and critical patients, and saliva taken from additional 31 mild/moderate patients who were not sampled for environmental contamination. the nurses and doctors who were taking care of these patients were also invited to participate into this study. infection control nurses swabbed the surfaces of their ppe, including coveralls (front and arm side), facepiece (front surface), gloves and bottom of shoe covers. hand swabs were also collected from some hcp before they did hand hygiene. an average of five samples were taken from each hcp. nurses also recorded the time since donning, exposure to aerosols, and incidence of spillover, if any. samples stored in vtm were immediately transported on ice to the laboratory of the bgi medical diagnostics company (wuhan) for rt-pcr tests of the open reading frame (orf) 1a/b genes of sars-cov-2. rna was extracted using the qiaamp viral rna mini kit and then proceeded with the rt-pcr kit (bgi biotechnology, wuhan) using the slan® realtime pcr system by hongshi technology (shanghai, china). the test results were also divided by highand low-touch surfaces near mild and severe/critical patients. blood samples were taken from the patients on the same day for tests of sars-cov-2 specific antibody igm and igg, using the kits of the wondfo biotech co., ltd (guangzhou, china), which had sensitivity of 86.4% and specificity of 99.6% for igg and igm (wondfo, 2020) . the titer higher than 10au/ml was regarded as positive. the classification of mild, severe and critical infections j o u r n a l p r e -p r o o f followed the national diagnosis criteria (china, 2020b). surface contamination rates were compared between the mild and severe/critical patient groups, and between seroconversion groups (igm or igg positive) using the fisher exact test. the significance level was set to 0.05. the ethical approval has been obtained from the ethics committee of the tongji hospital in huazhong university of science and technology. a total of 355 surface swabbing samples were collected from low-/high-touch surfaces near patients, hands and masks of patients, ppe of hcp while taking care of these patients. the detailed sampling sites are listed in supplementary table 2. one sample was found positive for sars-cov-2 in low-touch surfaces and 9 in high-touch surfaces. high-touch surfaces near severe/critical patients had a slightly higher contamination rate than those near mild patients (5.7% versus 2.4%, table 1 (table 1) . of 40 environmental samples from fever clinics and icu common areas (corridor and nursing stations), none tested positive. all of 20 swabs of door handle and keyboards and 17 air samples in clean areas also tested negative. we collected twelve air samples from patient rooms, with one near the air exhaust fan on the window and the rest within one meter of patients' head. only one sample was positive for sars-cov-2, which was collected within 10cm of a female patient while undergoing endotracheal intubation for invasive mechanical ventilation. one sample of cooling water from ventilator circuits was positive; suggesting regular thorough clean is needed for ventilator. two of nine severe or critical patients with sputum and saliva tested positive, and one saliva sample of 31 mild/moderate patients tested positive. all three also had sars-cov-2 detected in their throat samples on the same day. none of 36 surgical masks from 18 patients (14 mild and 4 severe/critical) had the rna of sars-cov-2 detected, though some patients have worn the same mask for 24 hours. for swabs from gloves, gowns, facepieces and bottom of boot covers worn by hcp inside dirty areas, all of 54 samples tested negative. none of the hand swabs from hcp were tested positive. in this study we collected a large number of surface swabs from various sites of isolation wards and icu after enhanced standard and transmission-based precautions. we also compared environmental contamination of low-and high-touch surfaces, patient hands and ppe of hcp, and the results were also linked to clinical data of sampling patients. a small j o u r n a l p r e -p r o o f proportion of samples (2.8%) were positive for sars-cov-2 in rt-pcr, which was much lower than those reported in an emergency field hospital in wuhan, china . the reasons could be the stringent ipc measures adopted in the ovb hospital. nevertheless, a slightly higher contamination rate was observed in high-touch surfaces than in low-touch surfaces, suggesting that environment decontamination shall focus more on these high-touch surfaces. we observed that severe/critical patients were slightly more likely to contaminate their surroundings, as compared to mild ones. most of these patients were 20 days after symptom onset, and 10 out of 24 patients (41.7%) still tested positive for sars-cov-2 using throat swabs on the day of sampling. the serology tests prior to or on the sampling date showed that nearly all were seroconverted (23/24 igg > 10au/ml, 18/24 igm > 10au/ml). this echoes the findings of a recent study in germany (wölfel et al., 2020) , which found that viral shedding continued after seroconversion. a recent study reported the rna of sars-cov-2 virus could be detected in faces as long as 47 days (wu y. et al., 2020) . unfortunately, we could not find whether viruses detected on surfaces were still viable, due to the lack of laboratory capacity for viral culture and quantitative pcr. therefore, it is unclear whether environmental contamination was correlated with viral loads of patients. the rna of sars-cov-2 virus could be detected in saliva and sputum of three patients (one severe/critical patient had both saliva and sputum positive), which is consistent with the previous reports (pan et al., 2020) . to our surprise, none of surgical masks worn by patients had positive results. another study found only 1 out of 14 surgical masks worn by mild and severe covid-19 patients tested positive for sars-cov-2 . this low positive rate is not statistically different from ours. we speculate the reason of negative results j o u r n a l p r e -p r o o f could also be due to low virus titers from these patients, as most of them were 30-40 days after symptom onset when sampling. laboratory studies showed that sars-cov-2 virus titers peaked 5-6 days post symptom onset and decreased to an undetectable level 8-10 days post symptom onset in most patients (he et al., 2020 , pan et al., 2020 , wölfel et al., 2020 . several studies have reported a longer period of detecting rna by rt-pcr in biological samples (particularly feces), compared to detecting viable viruses by viral culture (wölfel et al., 2020 , wu yongjian et al., 2020 . in this study, only one patient had diarrhoea, but none of the samples from the patient were positive, including five samples from bathroom surfaces. a study by liu et al collected air samples from different areas in one tertiary hospital and one fangcang shelter hospital in wuhan, the latter of which served as quarantine centers for mild covid-19 cases with limited medication treatment . they detected the rna of sars-cov-2 at low concentrations in the fangcang hospital, but not in the patient rooms of the tertiary hospital . another study in the aiir of a tertiary hospital in singapore also did not detect any virus in air samples (ong et al., 2020a) . similarly, in our study, only one air sample that was collected near patient during the endotracheal intubation procedure had sars-cov-2 detected. no virus was detected in additional 17 air samples from clean areas (staff offices), although isolation wards were not under negative pressure. our findings could support that natural ventilation together with extra air exhaust fans could efficiently reduce virus aerosols in patient rooms. it is of note that five surface swabs from the front side of facepiece and gloves of hcp who conducted aerosol-generating procedures (agp) for this were all negative. this highlights the importance of wearing proper ppe in agp. although we collected a large number of surface swabs from different parts of ppe, including the bottom of boot covers, none were positive in pt-pcr. another study also found a high contamination rate in three swabs from shoe sole of hcp, but none of the samples from other parts of ppe were positive . interestingly, studies in singapore detected the sars-cov-2 virus in surface swabs of front of shoes worn by hcp, but not in other parts of ppe as well (ong et al., 2020a , ong et al., 2020b . the transmission risk from hcp to patients appears low, since none of the ppe samples (except shoes) in these studies was found positive. but more frequent floor disinfection might still be necessary to further reduce the transmission risk in healthcare settings. two patients were found with hand contamination of the sars-cov-2 virus, which highlights the importance of hand hygiene education for patients. we placed one bottle of alcoholbased hand rub (abhr) near each ward entrance, and taught patients how to properly wash or rub their hands when they were admitted. if resources allow, ideally each patient should have one bottle near their bedside. none of the hcp were found to have their hands contaminated, which could be due to regular audits on hand hygiene compliance by the ipc team. there are several limitations in our study. first, this is a single center observational study; therefore, the result and protocol might not be generalized to other healthcare facilities, especially those with limited resources. second, although we collected a large number of samples, the number of patients recruited was relatively small. as the result, statistical power might not be enough for comparison across patient groups. third, the sensitivity and specificity of rt-pcr tests on surface contamination samples might not be same as those from human specimens. hence, false negative and positive results might have occurred in our samples. last but not least, it is unclear whether the virus was still viable on surfaces, since we did not culture the positive specimens. environmental contamination of the sars-cov-2 viral rna could be found even in seroconverted patients in healthcare settings, and the contamination risk was higher in high-touch areas near severe/critical patients. enhanced standard and transmission-based precautions should be maintained during the entire covid-19 pandemic period, to minimize the infection risk of hcp. covid-19 coronavirus pandemic managing mers-cov in the healthcare setting a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster fangcang shelter hospitals: a novel concept for responding to public health emergencies. the lancet prevention of nosocomial transmission of swine-origin pandemic influenza virus a/h1n1 by infection control bundle infection prevention and control guidelines for novel coronavirus in healthcare settings new coronavirus pneumonia prevention and control program aerosol and surface distribution of severe acute respiratory syndrome coronavirus 2 in hospital wards temporal dynamics in viral shedding and transmissibility of covid-19 severe acute respiratory syndrome: sars transmission of middle east respiratory syndrome coronavirus infections in healthcare settings seroprevalence of antibody to severe acute respiratory syndrome (sars)-associated coronavirus among health care workers in sars and non-sars medical wards a well infant with coronavirus disease 2019 (covid-19) with high viral load maternal and neonatal outcomes of pregnant women with covid-19 pneumonia: a case-control study aerodynamic analysis of sars-cov-2 in two wuhan hospitals surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) from a symptomatic patient absence of contamination of personal protective equipment (ppe) by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) viral load of sars-cov-2 in clinical samples the novel coronavirus originating in wuhan, china: challenges for global health governance transmission of 2019-ncov infection from an asymptomatic contact in germany temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study detection of sars-cov-2 in different types of clinical specimens virological assessment of hospitalized patients with covid-2019 virological assessment of hospitalized patients with covid-2019 prolonged presence of sars-cov-2 viral rna in faecal samples epidemiologic features and clinical course of patients infected with sars-cov-2 in singapore sars-cov-2 viral load in upper respiratory specimens of infected patients total surface included: low-touch surfaces, high-touch surfaces, hands of patients, masks, ventilator circuit and ppe of hcp. fisher exact test p-value = 0.577 between mild patients and severe/critical patients; p-value = 0.358 between patients with both antibodies positive (igm+ / igg+) and only igg positive (igm-/ igg+) lt, bm, xl, ly and xz originated and designed the study. jz, jf, qz, sw, zw and wp contributed to sample collection. lt, bm, xl contributed to data entry and clean. lh and pc key: cord-300583-0krbrj4w authors: koh, wee chian; naing, lin; wong, justin title: estimating the impact of physical distancing measures in containing covid-19: an empirical analysis date: 2020-08-13 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.026 sha: doc_id: 300583 cord_uid: 0krbrj4w background: epidemic modelling studies predict that physical distancing is critical in containing covid-19. however, few empirical studies have validated this finding. our study evaluates the effectiveness of different physical distancing measures in controlling viral transmission. methods: we identified three distinct physical distancing measures with varying intensity and implemented at different times—international travel controls, restrictions on mass gatherings, and lockdown-type measures—based on the oxford covid-19 government response tracker. we also estimated the time-varying reproduction number (r(t)) for 142 countries and tracked r(t) temporally for two weeks following the 100th reported case in each country. we regressed r(t) on the physical distancing measures and other control variables (income, population density, age structure, and temperature) and performed several robustness checks to validate our findings. findings: complete travel bans and all forms of lockdown-type measures have been effective in reducing average r(t) over the 14 days following the 100th case. recommended stay-at-home advisories and partial lockdowns are as effective as complete lockdowns in outbreak control. however, these measures have to be implemented early to be effective. based on the observed median timing across countries worldwide, lockdown-type measures are considered early if they were instituted about two weeks before the 100th case and travel bans a week before detection of the first case. interpretation: a combination of physical distancing measures, if implemented early, can be effective in containing covid-19—tight border controls to limit importation of cases, encouraging physical distancing, moderately stringent measures such as working from home, and a full lockdown in the case of a probable uncontrolled outbreak. coronavirus disease 2019 is an emerging respiratory infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (sars-cov-2), which was first detected in early december 2019 in wuhan, china. as of may 31, 2020, it has affected 5.93 million people and resulted in more than 367,000 deaths globally (who 2020) . in the absence of effective therapeutics or vaccines, containment measures rely on the capacity to control viral transmission through non-pharmaceutical interventions (npis) (kissler et al. 2020) . current evidence suggests that the effectiveness of case isolation and contact tracing strategies can be enhanced when combined with physical distancing measures in public settings (chu et al. 2020; kucharski et al. 2020) . governments worldwide have implemented various forms of physical distancing measure with varied stringency level and timeliness. the measures include school and workplace closures, cancellation of public events, restrictions on mass gatherings, public transport closures, stayat-home orders, restrictions on internal movements, and international travel controls. due to the potential for socioeconomic disruptions caused by these measures, it is therefore important to quantify their impact on disease spread to inform policymaking, which has thus far relied primarily on epidemic modelling studies (ferguson et al. 2020; prem et al. 2020) . as cases accumulate, it has become possible to use empirical data derived from real-world observations to validate the model-based estimates of the effectiveness of policy interventions. in this paper, we assessed-at a normalized point on the epidemic curve-the impact of physical distancing measures on viral transmission measured by the time-varying reproduction number, rt, which represents the expected number of secondary cases generated by a primary case at time t. a value of rt greater than one indicates that a sustained outbreak is likely. the goal of policy intervention is to bring rt below one, suggesting that the outbreak is under control. data on physical distancing measures were obtained from the oxford covid-19 government response tracker (oxcgrt), which collects information, starting from january 1, 2020, on a range of government policies, assigns a stringency score for the measures, and aggregates the data into a common index for 170 countries (may 28 version). we used the stringency index as an aggregate measure, which has a score between 0 and 100, with a higher index indicating increased stringency. we further examined the impact of specific measures: (i) school closures; (ii) workplace closures; (iii) cancellation of public events; (iv) restrictions on size of gatherings; (v) public transport closures; (vi) stay-at-home orders; (vii) restrictions on internal movements, and (viii) restrictions on international travel. these measures have an ordinal scale of severity or intensity. further details on the oxcgrt database are provided in hale et al. (2020) . we normalized the stage of disease spread to minimize the confounding effect of increased caseload on transmission: the impact of interventions is expected to be different at 10 and 1,000 cases. we used 100 total cases as the starting point for all countries to indicate an outbreak (hartfield and alizon 2013) . we estimated rt for 142 countries that have reported at least 100 cases as of may 28, 2020. the estimation covered the whole period from the first reported case to may 28 using a weekly sliding window based on the methods developed by cori et al. (2013) . we used data on new daily cases and the distribution of the generation time (time between infection of an index case and infection of a secondary case). we incorporated uncertainty in the generation time distribution with a mean of 3.6 days (sd: 0.7 days) and standard deviation of 3 days (sd: 0.8 days) and used a gamma prior for the reproduction number with mean 2.6 and standard deviation 2. these parameter estimates were obtained from the covid-19 epiforecasts project by the centre for the mathematical modelling of infectious diseases at the london school of hygiene and tropical medicine (see abbott et al. 2020) . data on daily reported cases were obtained from the european centre for disease prevention and control and from the johns hopkins university centre for systems science and engineering covid-19 data depository. rt was estimated using the epiestim package in r version 3.6.3 (r foundation for statistical computing). an important feature of examining rt, instead of cumulative case numbers, is that, if the proportion of cases that are unreported remain constant throughout an outbreak, estimates of rt are unaffected by underreporting (thompson et al. 2019) . as countries have implemented and subsequently relaxed measures in response to the outbreak, establishing causality from such measures to a change in rt is challenging. to address possible reverse causality, we examined the measures that were in place at the time when 100 cases have been reported. we then tracked the median rt temporally over the next 14 days. the lagged measures thus controls for the endogenous response to viral transmission. we regressed rt on physical distancing measures and other covariates. the control variables used were income level (log of gdp per capita at current us$), population density (log of population per square kilometre), age structure (proportion of population aged 65 years and above), and air temperature (14day average after the 100 th case). these socioeconomic and environmental factors have been postulated to influence disease spread qiu et al. 2020) . data on gdp per capita, population density, and population above 65 years old were obtained from the world bank's world development indicators, supplemented by the central intelligence agency's the world factbook. data on temperature were collected from the air quality open data platform and other online weather resources. the empirical specification takes the following form: is the average reproduction number of country over the 14 days following the date of the 100 th case; is country 's physical distancing measure of type on the date of the 100 th case; represents the country characteristic (income level, population density, age structure, and temperature) of country ; is a constant term, 's are the regression coefficients, and denotes the error term. a schematic of the methodology is outlined in figure s1 in the supplementary materials. we also conducted ex-post predictions on the date of the 100 th case using equation (1) to make comparative assessments on how rt would be predicted to evolve relative to what has been observed in reality. all regression analyses were performed in stata 14 (statacorp llc). j o u r n a l p r e -p r o o f 8 we conducted a series of robustness checks to validate our results. we explored a shorter time horizon of seven days to address the possibility of new measures implemented after the 100 th case that could affect rt. we also used the growth in total cases instead of rt as the dependent variable. to examine actual behavioural changes instead of de jure government policies, we used a de facto measure of physical distancing using mobility data from google community mobility reports. we first take a cursory look at the nature of the relationship between physical distancing measures and rt, and then proceed to estimate the magnitudes using regression models. the average timing of implementation of the physical distancing measures is summarized in table s1 in the supplementary materials. the earliest policies to be implemented, on average, were restrictions on international travel, about 11 days before the detection of the first case. cancellation of public events and school closures were the initial responses during the onset of an outbreak (about a week after the first case), followed by restrictions on the size of gatherings and more stringent measures such as workplace closures, restrictions on internal movement, stay-at-home orders, and public transport closures. on average, all these measures were implemented before the occurrence of the 100 th case. since several measures were implemented very close to one another, and due to the similar nature of some the measures, it is difficult to relate the observed changes in rt to a specific measure. we addressed this identification issue by grouping the measures, taking into account the implementation timing and correlation ( [ figure 2 here] j o u r n a l p r e -p r o o f the time-varying reproduction number rt is the expected number of secondary cases generated by a primary case at time t. the specific measures on international travel restrictions are detailed in table 1 . each bubble represents a country, and the size of the bubble is proportional to the total number of reported cases as of may 28, 2020. [ figure 3 here] the time-varying reproduction number rt is the expected number of secondary cases generated by a primary case at time t. the specific measures on mass gathering restrictions are detailed in table 1 . each bubble represents a country, and the size of the bubble is proportional to the total number of reported cases as of may 28, 2020. table 1 . each bubble represents a country, and the size of the bubble is proportional to the total number of reported cases as of may 28, 2020. we first examine the impact of the stringency index on rt. the results are reported in column (1) of [ table 3 here] to validate our results, we conducted several robustness checks. we tracked rt over seven days and used the growth of total cases instead of rt as the dependent variable. we also used a de facto measurement of physical distancing using google mobility data-as opposed to de jure government announced measures-to examine the actual observed behaviour changes on rt. the findings are largely unchanged, as reported in columns (2) to (4) in table 2 and the supplementary materials (tables s3 and s4 , figure s2 ). we conducted ex-post predictions using the regression model in column (4) of table 3 to retrospectively assess how rt would be predicted to evolve over the following two weeks, given the case history and physical distancing measures implemented on the date of the 100 th case, along with specific country characteristics. the predicted rt of the 142 countries are displayed in table s5 in the supplementary materials. some countries had a lower rt over the two weeks following the 100 th case than predicted by the model, such as japan, brunei, iceland, and vietnam. by contrast, others, such as turkey, italy, and the united states had a higher rt. we assessed, at a standardized stage of the outbreak at 100 cases, the impact of physical distancing measures on covid-19 transmission, measured by rt, and found that, on average, they have been our study provides empirical support to findings from modelling studies that highlight the role of physical distancing measures in containing covid-19. we identified three distinct measures, implemented at different times-restrictions on international travel prior to the first reported case, restrictions on mass gatherings during the onset of an outbreak, and lockdowns at later stages. our analysis suggests a hierarchy of physical distancing measures that are effective in outbreak control. we found that lockdown-type measures had the largest effect on limiting viral transmission, followed by j o u r n a l p r e -p r o o f complete travel bans. these measures have to be implemented early to be effective-based on our definition of early implementation using the observed median timing across countries worldwide, lockdown measures are considered early if they were instituted about two weeks before the 100 th case and travel bans a week before detection of the first case. this accords with the findings in other studies that severe travel restrictions have been critical in slowing down infections in china and around the world (keita 2020) , and also corroborates studies showing that lockdowns limited disease spread in wuhan (fang et al. 2020) , italy and spain (tobias 2020) , and california (friedson et al. 2020) . importantly, our findings suggest that lockdowns measures should not be viewed in a binary approach. there is a wide range of lockdown-type measures from less stringent forms such as working from home up to complete movement restrictions, and all were shown to be effective in suppressing viral transmission. if implemented early, work from home and stay at home recommendations reduce rt by 0.45 (95% ci: -0.82, -0.07); a partial lockdown reduces rt by 0.38 (95% ci: -0.72, -0.04); and a complete lockdown reduces rt by 0.32 (95% ci: -0.55, -0.09). across these three grades of lockdown-type measures, the 95% ci of their effect sizes overlap suggesting no significant difference in effectiveness across these measures. this finding is replicated even when assessed against other indicators of outbreak control, such as the increase in cumulative cases. as such, we suggest that early on in the outbreak, complete lockdowns may be unnecessary to control viral transmission, given the availability of other equally effective and more sustainable approaches. this is particularly important for the poorest countries. more than four-fifths of low-and lower-middle income countries have imposed complete lockdowns at the time of 100 reported cases (compared to three-fifths in upper-middle income and less than one-third in high-income countries), with potentially severe socioeconomic consequences, having already been hit by the slump in global economic activity, including sharp declines in remittances, tourism receipts, and commodity revenues (world bank 2020). measures that recommend workplace closures or staying at home have been effective, implying that voluntary physical distancing has played an important role. in the united states, the decrease in mobility has been found to be largely voluntary, reflecting greater awareness of risk (maloney and taskin 2020). japan has achieved success without the need for a complete lockdown. clear public health messaging and voluntary practice of physical distancing shaped by cultural norms such as mask wearing, avoiding handshakes, and keeping silence when taking public transport and during events such as funerals, have been critical in limiting disease spread (sposato 2020) . overall, our analysis suggests that a combination of physical distancing measures may yield the most beneficial outcomes: international travel restrictions to limit imported cases from high-risk regions, encouraging voluntary social distancing, moderate forms of lockdown-type measures such as working from home and only leaving the house for necessary activities, and complete lockdowns in areas or provinces with more severe outbreaks. the implementation timeliness of these measures invariably depends on the country-specific context, including public acceptance and institutional capacity. countries that have been relatively successful share these common elements. despite an international travel hub and its close proximity to wuhan, early border control and the practice of personal protective behaviours, including the use of face masks, contributed to hong kong's success in controlling viral transmission (wong et al. 2020) . taiwan and brunei responded quickly by instituting border control and reassured the public by delivering timely information on the epidemic (wang et al. 2020; wong et al. 2020) . targeted lockdown-type measures in vietnam, coupled with mask wearing and consistent public health messaging, helped to contain disease spread (duc huynh 2020) . our study has several limitations. first, although we controlled for several country characteristics, our model could suffer from omitted variable bias as behavioural variables, such as mask wearing, were unaccounted for due to lack of data. second, beyond physical distancing measures, other npis such as j o u r n a l p r e -p r o o f early case isolation and aggressive contact tracing and quarantine are critical elements of a successful containment strategy (ferguson et al. 2020) , which we could not control for, again due to the lack of data. third, although a significant amount of effort has been put into the construction of the oxcgrt database with a global coverage and a systematic classification of government policies, there could be some reporting errors or data quality issues. moreover, our country-level analysis may miss the variation of policies implemented at the city/county/province level. nonetheless, the database is the most comprehensive to date. physical distancing measures have been applied in arguably every country that is fighting covid-19. although modelling studies have shown the importance of physical distancing in stemming disease spread, few empirical studies have validated this finding. we provide empirical support and quantified the impact of physical distancing measures in lowering the reproduction number, particularly lockdowntype measures and border closures. moreover, we found that less stringent lockdown-type measures, such as encouraging working from home and staying home unless necessary were as effective as complete lockdowns in reducing transmission. however, all these measures have to be implemented early to be effective. as many countries are in the midst of de-escalating, we suggest that some combination of these measures-empirically justified-should be considered in containing subsequent waves of covid-19. j o u r n a l p r e -p r o o f and jw wrote the manuscript with critical feedback from ln. all authors contributed to and approved the final manuscript. this research did not receive any specific grant from funding agencies in the public, commercial, or notfor-profit sectors. not required. pandemic ? cmaj 2020; 192(19) : the dependent variable is the average rt over the 14 days since the date of the 100 th case. rt, the timevarying reproduction number, is the expected number of secondary cases generated by a primary case at time t. the physical distancing measures are those that are in place on the date of the 100 th case; refer to table 1 for the specific measures. standard errors are in parenthesis. ***, **, and * represents statistical significance at the 1%, 5%, and 10% level respectively. n/a denotes not available. estimating the time-varying reproduction number of sars-cov-2 using national and subnational case counts covid-19: cross-country heterogeneity in effectiveness of nonpharmaceutical interventions physical distancing, face masks, and eye protection to prevent person-to-person transmission of sars-cov-2 and covid-19: a systematic review and meta analysis. the lancet a new framework and software to estimate time-varying reproduction numbers during epidemics the effect of containment measures on the covid-19 pandemic the covid-19 containment in vietnam: what are we doing? human mobility restrictions and the spread of the novel coronavirus (2019-ncov) in china. nber working paper 26906 report 9 -impact of nonpharmaceutical interventions (npis) to reduce covid-19 mortality and healthcare demand did california's shelter-in-place order work? early coronavirus-related public health effects. nber working paper 26992 variation in government responses to covid blavatnik school of government working paper 2020/032. university of oxford introducing the outbreak threshold in epidemiology air passenger mobility, travel restrictions, and the transmission of the covid-19 pandemic between countries projecting the transmission dynamics of sars-cov-2 through the postpandemic period early dynamics of transmission and control of covid-19: a mathematical modelling study impact of meteorological factors on the covid-19 transmission: a multi-city study in china determinants of social distancing and economic activity during covid-19: a global view the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study impacts of social and economic factors on the transmission of coronavirus disease 2019 (covid-19) in china japan's halfhearted coronavirus measures are working anyway. foreign policy improved inference of time-varying reproduction numbers during infectious disease outbreaks evaluation of the lockdowns for the sars-cov-2 epidemic in italy and spain after one month follow up response to covid-19 in taiwan: big data analytics, new technology, and proactive testing coronavirus disease (covid-19) situation report -132. geneva: world health organization journal of global health. 2020. 100 th case; rt,7 in column (2) is the average rt over the 7 days following the date of the 100 th case; g in column (3) is the growth rate of total cases between the date of the 100 th case and the date 14 days later. the stringency index is a composite index of physical distancing measures with a range of 0 to 100 mobility (from google community mobility reports) is the average percent change in visits to retail and recreation, grocery and pharmacy, parks, transit and workplaces on the date of the 100 th case compared to the median baseline value of the corresponding day of the week during standard errors are in parenthesis. ***, **, and * represents statistical significance at the 1%, 5%, and 10% level we thank dr ying-ru lo, head of mission and who representative to malaysia, brunei darussalam and singapore, for useful comments and suggestions.j o u r n a l p r e -p r o o f all authors have no conflict of interest to declare. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-290100-wnjjqqn5 authors: wong, samuel y.s.; kung, kenny; wong, martin c.s.; wong, carmen; tsui, wendy; chan, king; liang, jun; lee, nelson l.s.; cheung, annie w.l.; wong, eliza l.y. title: primary care physicians’ response to pandemic influenza in hong kong: a mixed quantitative and qualitative study date: 2012-07-11 journal: int j infect dis doi: 10.1016/j.ijid.2012.03.015 sha: doc_id: 290100 cord_uid: wnjjqqn5 objectives: the current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza a h1n1 virus in hong kong in 2009. methods: a cross-sectional survey was conducted of 300 doctors working in public primary care clinics. in addition, a qualitative study was conducted in two selected general outpatient clinics (gopcs) with 10 doctors between september and december 2009. results: we found that there was an increase in clinical service demand for public primary care doctors and that there was lower compliance with hand washing as compared to the wearing of masks among gopc doctors during the study period. conclusions: since hand hygiene and influenza vaccination are effective methods to prevent the spread of influenza infection, future studies should explore the reasons for non-compliance with these preventive behaviors among doctors. more education and training in dealing with influenza a h1n1 infection may be needed. in april 2009, the influenza a h1n1 virus surfaced and spread rapidly across the globe. on june 11, 2009 , the world health organization (who) declared a pandemic caused by the influenza a h1n1 virus. in any healthcare system, primary care is at the forefront of the response to any emerging epidemic. since the outbreak of severe acute respiratory syndrome (sars), 1 there has been a growing recognition of the need for an integrated preparedness approach to deal with public health threats, to include acute clinical care, public health, and emergency management systems. 2 preparing for health threats is particularly important in primary care -the first point of contact for patients entering the healthcare system. in 2008, patel et al. 3 developed a framework that can be used to facilitate the systematic planning of the primary care response to pandemic influenza and to appraise the coverage of key elements in the preparedness to deal with a pandemic. this framework consists of four functional domains that include clinical care, the internal and macro-environment of the primary care/general practice, and the public health responsibilities of doctors. these functional domains were first identified by the authors through a review of the peer reviewed and gray literature that included strategies relevant to general practice at the time of an influenza pandemic, and the framework was later validated through interviews with general practitioners and practice nurses and senior decision-makers. it was subsequently used to evaluate 89 publicly available jurisdictional plans in five countries. 3 since the provision of primary care is organized differently in different countries, studying how each primary care system responds to a pandemic may generate transferable learning for other primary care systems. recent research has studied the knowledge, attitudes, and practices, or vaccination acceptability in dealing with an influenza a h1n1 pandemic among primary care practitioners in singapore, 4 australia, 5 france, 6 and the netherlands. 7 however, few studies have been conducted using a previously developed framework to evaluate the response of primary care to an influenza a h1n1 pandemic before the escalation of the pandemic alert and during the influenza a h1n1 pandemic. the current study was conducted to use a developed framework to appraise the public primary care response to pandemic 2009 influenza a h1n1 virus in hong kong in 2009. to better understand the responses of primary care doctors to the influenza a h1n1 pandemic, both a quantitative survey and a qualitative study were conducted. the peak activity of the pandemic h1n1 virus in hong kong occurred during july through september 2009. this was also the time when our survey study was conducted. from july 20, 2009 to august 18, 2009 , 300 questionnaires were mailed to doctors who worked in 54 general outpatient clinics (gopcs) distributed across five major geographical clusters in hong kong: 11 in the new territories east cluster, 8 in the new territories west cluster, 6 in the kowloon central cluster, 23 in the kowloon west cluster, and 6 in the hong kong west cluster. in hong kong, the hospital authority manages all government run gopcs in primary care in seven geographic clusters. the role of the gopcs is to provide access to quality clinical care in the form of primary care services to the financially vulnerable, the elderly, and patients with chronic diseases. most gopcs are located in the community and are often the first point of contact with public clinics among the elderly and the financially vulnerable. ethics approval for this study was granted by the survey and behavioural research ethics committee of the chinese university of hong kong. using an anonymous questionnaire, primary care doctors who worked in these clinics were asked to report four domains of primary care practice with respect to a published framework for planning to cope with pandemic influenza in primary care. the questionnaire was developed to include five major domains of primary care practice that have been found to be relevant in the planning to manage pandemic influenza. these include: (1) changes in clinical services and clinical care for influenza; (2) changes in the internal environment of primary care practice such as preventive behaviors of doctors, including hand washing and wearing a mask; (3) changes in the macro-environment of primary care practice such as the use of guidelines, training, or measures; (4) public health responsibilities such as in primary care; and (5) the impact of influenza a on quality of life, assessed using three questions: ''has influenza affected the quality of your life?'', ''did you feel depressed in the past 2 weeks?'', and ''did you feel emotionally stressed in the past 2 weeks?''. the questionnaire had a multiple choice design and the respondents could tick one or more of the alternatives. moreover, the primary care practitioners were asked about whether they would be willing to be vaccinated when a vaccine was available. the survey also included questions on demographics such as age and sex, as well as educational background, postgraduate qualifications, and the type of clinic the doctor worked in. a sample of the questionnaire is provided as supplementary material. the questionnaire was piloted on 30 primary care practitioners before the actual distribution, and modifications were made as a result of the comments and suggestions received from the primary doctors. to further explore the responses of primary care physicians to pandemic influenza in hong kong, individual interviews were conducted among physicians at two randomly selected gopcs. the interviews were conducted using a discussion guide covering two areas: workload during pandemic influenza and the acceptance of influenza vaccination. to allow a greater expression of views on these sensitive issues, individual interviews were used instead of focus groups. ten individual interviews were conducted in the selected gopcs until data saturation was reached. descriptive statistics are presented. chi-square tests were used for the analyses of categorical variables, and analysis of variance was used for continuous variables. an analysis was performed to explore the relationships between having encountered patients with suspected influenza a h1n1 and the responses to the five domains in the clinical services questionnaire using chi-square statistics. all statistical analyses were performed using spss for windows v. 16 .0 (spss, chicago, il, usa), and the level of significance was set at 5%. for the qualitative study, the content of individual interviews was transcribed and coded using nvivo 7.0. data were analyzed by two independent researchers (elyw and awlc) based on the discussion guide. during the analysis, data within themes were scrutinized for agreement in views across the range of participants. of the 300 questionnaires sent to the primary care doctors of gopcs, 126 were completed and returned, giving a response rate of 42%. demographic information for the doctor respondents is shown in table 1 . since there is no primary care registry in hong kong, we were unable to compare the demographic information of the respondents to those of the rest of the primary care doctors in hong kong. when compared to the findings of the 2009 health manpower survey on all registered doctors, we found a higher proportion of female doctors in our survey than in the health manpower survey (57% male and 43% female as compared to 72% male and 28% female). the mean age of doctors in our survey was 36 years as compared to a median age of 45 years in the health manpower survey. in our survey, 96% of doctors worked full time and 77% had a postgraduate qualification, with 55% having a diploma in family medicine, 10% a masters in family medicine, and 44% a fellowship in family medicine. with respect to changes in clinical services, 59% of participating gps noticed a higher demand for services. moreover, the majority (86%) stated that influenza a h1n1 had affected their clinical practice; 88% of these doctors reported testing patient temperature as a routine procedure and 76% insisted every patient wear a mask during consultations. among all respondents, 63% stated that they had encountered a patient suspected of influenza a h1n1. among the suspected cases, around 20% were laboratory confirmed. with respect to changes in the internal environment of practice, 94% of participants stated that they always wore a mask during consultations before the influenza a h1n1 epidemic and this percentage increased to 99% during the epidemic. similarly, 45% of participants stated that they washed their hands between or before patient encounters before the epidemic, while at the time of the survey (during the pandemic), 54% of them stated that they washed their hands between or before patient encounters (p < 0.001). other precautions, in addition to hand washing and the wearing of a mask, included asking all cleaning staff to wear masks (76%), cleaning the work surfaces with antiseptics (70%), and asking staff to check their temperature before going to work (60%). moreover, 73% of the clinics required nursing/reception staff to wear masks before the epidemic, and during the pandemic, 97% of clinics required reception staff to wear masks. among the respondents, 42% stated that they would have the influenza a h1n1 vaccination when it was available. the majority stated that they would not have the influenza vaccination and the reasons given for this were: (1) they did not trust the effectiveness of the new vaccine (57%), and (2) they did not think it is necessary (30%). the majority of participating doctors stated that the intranet and other communication channels at the clinics they worked for (56%) were their most likely sources of updated information on influenza a h1n1, followed by correspondence from the government or semi-government organizations (38%). with respect to the macro-environment of primary care practice, 71% of doctors who participated in this survey used guidelines to assist them in making clinical decisions and 56% of these doctors had received training on the use of guidelines. however, 62% continued to want more professional education regarding how to deal with h1n1 influenza. the majority of doctor participants were satisfied with the measures the government had implemented to prevent influenza a h1n1 from spreading in the community and more than half would have liked to have had more involvement in the management of influenza a h1n1 in the community (57%). with respect to public health responsibilities, more than half (59%) of the doctors had not participated in surveillance activities associated with acute respiratory infections. among those who had, 58% reported suspected cases of influenza a h1n1 to the government. on a scale of 0-100 for 'not affected at all' to 'extremely affected', around 29% of doctor respondents scored 50 or above on the scale with the question, ''has influenza a h1n1 affected the quality of your life?''. on a scale of 0-100 for 'not depressed at all' to 'extremely depressed', around 14% of doctor respondents scored 50 or above on the scale with the question, ''did you feel depressed in the past 2 week?''. on a scale of 0-100 for 'not stressed at all' to 'extremely stressed', 27% of doctor respondents scored 50 or above on the scale with the question ''did you feel emotionally stressed in the past 2 weeks?'' 3.1.6. relationships between having encountered patients with suspected influenza a h1n1 and the five domains of practice in our analyses on the relationships between having encountered patients with suspected influenza a h1n1 and clinical service (table 2) , a significantly higher proportion of doctors who had encountered patients with suspected influenza a reported seeing more patients than those who had not encountered such patients (71% vs. 38%; p < 0.001). they were also more likely to have used guidelines when making clinical decisions (77% vs. 60%; p = 0.055) and were more likely to have participated in surveillance activities (54% vs. 16%; p < 0.001). in addition, they were also more likely to have felt emotionally stressed in the past 2 weeks when compared to those who had not encountered a suspected influenza a infection (mean score: 38.3 vs. 22.4; p = 0.001). in terms of training, they were more likely to have a postgraduate qualification (83% vs. 67%; p = 0.052) and were more likely to be a family medicine specialist (47% vs. 26%; p = 0.055). twelve individual interviews were conducted among physicians in two selected gopcs between september and december 2009. two themes were explored: increased workload and attitudes towards influenza vaccination. the majority commented on the increased workload and the long working hours during the influenza pandemic, because they had to work on current pre-booked chronic cases and also new fever cases. in addition, there was no quota limit for 'walk in fever case'. a typical comment was as follows: ''though the office hour is until 5 p.m. but there are still a lot of patients lining up at 5 p.m., we must accept them. . .unlimited quota but limited manpower. . .'' (c1) also, some physicians revealed that they were too busy to wash their hands between patient consultations: ''there are many patients walking in for fever consultation, the clinic is open during lunch time as well. . .and we are even too busy to wash hand. . .'' (c3) the majority of the physicians agreed to having an influenza vaccination, which was regarded as a healthcare professional's responsibility. however some participants hesitated to receive the swine flu vaccination because of queries regarding efficacy and side effects. some expressed the view that the swine flu vaccination was not necessary because they had already contracted swine flu: ''i will receive the vaccination because it is healthcare professional's responsibility. . .to protect ourselves. . .to protect public. . .'' (c7) ''vaccination for swine flu is still new. . .i will wait to see the efficacy and side effect from more clinical trial'' (c11) ''vaccination may not be necessary. . .because some of us have been contracted from swine flu already. . .even my family members have contracted already'' (c33) in this survey, we found that a significant proportion of public doctor respondents reported an increase in workload as a result of the influenza a h1n1 pandemic. indeed, one fifth of them stated that they had increased their office hours to cope with the higher demand for services. with regard to changes in the internal environment of practice, the majority of doctors (99%) who responded to the survey reported that they had always worn a mask during consultations in the past 3 days, although the proportion who had always washed their hands between/before consultations in the past 3 days was much lower (54%). the lower proportion of doctors who reported always having washed their hands between/before consultations in the past 3 days could be a concern, as previous studies have demonstrated that hand hygiene is an effective method to prevent the transmission of influenza and that hand washing is one of the effective methods to reduce an influenza pandemic. [8] [9] [10] the reasons for the lower self-reporting of hand washing between patients when compared to wearing masks are unknown, but we can speculate that this could be due to the fact that more time and effort is required for washing hands between patients as compared to wearing a mask. this is further supported by findings from our qualitative study, which showed that doctors might have been too busy to wash their hands between patients. almost half of the respondents (42%) reported that they were willing to have the influenza a vaccination, and for the other respondents the two most common reasons for refusal to have the vaccine were not trusting the effectiveness of the new vaccine and not thinking it necessary. these findings were further confirmed by the data from our qualitative study. moreover, the additional reason of thinking that they had already been infected with influenza a h1n1 might have further reduced the willingness to accept the influenza a h1n1 vaccination. these findings among doctors in our study are similar to those recently reported in hong kong among hospital healthcare workers, which showed community nurses having the lowest willingness to accept vaccination. 11 starting in 2010, all seasonal influenza vaccines have included the swine flu component. whether this will help to ease some fear is unknown. of note, current available surveillance data suggest no increase in adverse events with swine flu vaccines compared to seasonal flu vaccines. 12 acceptability of pandemic influenza vaccination was found to be higher in studies conducted in general practice in france and the netherlands, at 60% and 80%, respectively. 6,7 similar to findings from previous studies on the same issue, the major concerns for both nurses and doctors with respect to influenza a h1n1 vaccination were fear of side effects and concerns regarding the efficacy of the new vaccine. 6, 7, [11] [12] [13] [14] annual vaccination against influenza has been considered to be the best way to reduce sickness and death from influenza in high-risk populations, to reduce absenteeism from work in healthy adults, and to minimize healthcare-associated transmission of influenza. [15] [16] [17] with respect to the use of guidelines in dealing with pandemic influenza and the need for further training and education for dealing with pandemic influenza, we found that more than half of the doctors who worked in public clinics were likely to use guidelines (71%), but at the same time wanted to have more training on how to deal with pandemic influenza (62%). the high proportion of public doctor respondents who reported using guidelines could likely be due to the use of an intranet within large organizations, or more standardized behavior among employees in the same organization, although this is not supported by findings from our community nurses. despite the reported use of guidelines by healthcare workers, a significant proportion continued to state the need for more training in dealing with influenza a h1n1. with regard to assuming public health responsibilities, the rate among public doctors was 41%. we could speculate that this is due to the more standardized instructions or supervision among doctors who work in the same organization as compared to doctors who work in private settings who may work solo or work in small groups. not surprisingly, among doctors who had encountered a suspected influenza a h1n1 infection, a higher demand for services and higher emotional distress in the past 2 weeks were reported when compared to those who had not encountered a suspected influenza a h1n1 infection. increased stress related to dealing with novel infections has been reported previously and our findings are consistent with previous findings. 4, 18 moreover, we found that doctors who reported having more training in family medicine were more likely to have reported suspected influenza a h1n1 infections. whether this is due to the greater training received, which increased their awareness and alert in detecting or suspecting influenza a h1n1 infections in patients, is unknown, but as a group we failed to find any significant differences in terms of protective behaviors such as washing hands or wearing masks in the past 3 days, or having an influenza vaccination, between those with and without postgraduate qualifications. a major limitation of the survey was the low response rate. thus, we are unsure about the representativeness of the results from these studies. an additional limitation is that we have only analyzed self-reported behaviors and attitudes. we did not directly observe their behavior and there could have been a social desirability bias for respondents to have a 'better' response in order to look good, especially among those in public clinics. public community doctors responded that they would like to have more education and training for dealing with pandemic influenza. future policies from the government should look into the educational needs of healthcare workers to increase their confidence in dealing with influenza pandemics. another finding was the lack of willingness of healthcare workers to have the pandemic influenza vaccination. future work to determine effective interventions to increase uptake, which may include designing interventions based on the ecological model, is called for; the need to address low influenza vaccination rates in this high-risk group is urgent in the context of a pandemic response. another key finding was the low level of compliance of the doctor respondents with hand washing between patients. due to the possibility of social desirability bias, we believe that the rate of hand washing may have been even lower than that reported in this study. as shown in the results, this low rate of hand washing between patients could have been a bigger problem. more education may be needed or more research is needed to explore the reasons for the lack of hand washing among frontline doctors, which may put both doctors and patients at risk of cross-infection. monitoring community responses to the sars epidemic in hong kong: from day 10 to day 62 public health preparedness: a system level approach general practice and pandemic influenza: a framework for planning and comparison of plans in five countries a crosssectional study of primary care physicians in singapore on their concerns and preparedness for an avian influenza outbreak attitudes amongst australian hospital healthcare workers towards seasonal influenza and vaccination positive attitudes of french general practitioners towards a/h1n1 influenza pandemic vaccination: a missed opportunity to increase vaccination uptakes in the general public? high vaccination rates for seasonal and pandemic (h1n1) influenza among healthcare workers in dutch general practice facemasks and hand hygiene to prevent influenza transmission in households physical interventions to interrupt or reduce the spread of respiratory viruses: systematic review non-pharmaceutical public health interventions for pandemic influenza: an evaluation of the evidence base willingness of hong kong healthcare workers to accept pre-pandemic influenza vaccination at different who alert levels: two questionnaire surveys press release: review of pandemic vaccines underway influenza vaccination among primary healthcare workers which determinants should be targeted to increase influenza vaccination uptake among healthcare workers in nursing homes? prevention and control of seasonal influenza with vaccines: recommendations of the advisory committee on immunization practices (acip) the effectiveness of vaccination against influenza in healthy, working adults influenza vaccination of healthcare workers and vaccine allocation for healthcare workers during vaccine shortages longitudinal assessment of community psychobehavioral responses during and after 2003 outbreak of severe acute respiratory syndrome in hong kong this study was supported by the research fund for the control of infectious diseases (rfcid), food and health bureau, hong kong sar government.conflict of interest: the authors declare that they have no competing interests. supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.ijid.2012.03.015. key: cord-265146-j0n3a4m6 authors: hsieh, ying-hen title: ascertaining the 2004–2006 hiv type 1 crf07_bc outbreak among injecting drug users in taiwan date: 2013-02-12 journal: int j infect dis doi: 10.1016/j.ijid.2013.01.002 sha: doc_id: 265146 cord_uid: j0n3a4m6 objective: to ascertain the explosive 2004–2006 outbreak of hiv-1 crf07_bc among intravenous drug users (idu) in taiwan, which more than doubled the total number of reported hiv cases in less than 3 years, resulting in a 45-fold increase in cumulative idu/hiv cases and a 40-fold increase in previously seldom-reported female idu/hiv cases. methods: a mathematical model was utilized to fit the monthly case data, in order to estimate the turning points (peak incidence) and the reproduction number r of the outbreak. furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female idus. results: model fit revealed a two-wave epidemic during april 2004–march 2007. the larger second wave started shortly after may 2005 and peaked in october 2005 before gradually subsiding. r was estimated to be 3.15 (3.14–3.16) and 27.21 (26.73–28.05) for the two respective waves. the time series of monthly differences in male and female case data were found to be most significantly correlated at lag 0 (i.e., r > 0.7) with r = 0.906 and 0.804, respectively in each direction. the granger causality test indicated that the male time series caused the corresponding female time series with a lag of 2 months or less. conclusions: the modeling results revealed the presence of a small first wave in 2004, before an explosion of cases after may 2005. furthermore, a harm reduction program implemented in august 2005 contributed to the downturn in the epidemic after october. correlation results also suggest that the upsurge in male hiv cases led to the subsequent drastic surge in female cases. in taiwan, where active hiv/aids surveillance has been in place since 1996, with 2.1-2.5 million annual screening tests and free antiretroviral therapy (art) introduced since 1997, [1] [2] [3] [4] during this time-period, an outbreak of hiv-1 crf07_bc infections among idus, including many previously seldom-seen female idu hiv-infected cases, resulted in more reported cases than all reported hiv cases among all risk groups combined in the previous 20 years since 1984, when the first aids case was reported. it has been speculated that the source of this outbreak was a drugtrafficking route to taiwan from yunnan province via southeast china, guangxi province, and hong kong, [6] [7] [8] from where a substantial amount of heroin was being smuggled into taiwan. moreover, five idus from southern taiwan were diagnosed as the country's first hiv-1-seropositive cases infected with crf07_bc in 2002. 2 it has been reported that the percentage of persons receiving a diagnosis of aids within 12 months of diagnosis of hiv infection dropped suddenly from 20% in 2003 to 8.3% in 2005, during the time when most of the newly diagnosed cases came from the idu population, which implies that the detected idu cases were in the early stage of hiv infection. 4 it has also been reported 1 that 96% of objective: to ascertain the explosive 2004-2006 outbreak of hiv-1 crf07_bc among intravenous drug users (idu) in taiwan, which more than doubled the total number of reported hiv cases in less than 3 years, resulting in a 45-fold increase in cumulative idu/hiv cases and a 40-fold increase in previously seldom-reported female idu/hiv cases. methods: a mathematical model was utilized to fit the monthly case data, in order to estimate the turning points (peak incidence) and the reproduction number r of the outbreak. furthermore, correlation analysis was carried out to assess the correlation between infections among the male and female idus. results: model fit revealed a two-wave epidemic during april 2004-march 2007. the larger second wave started shortly after may 2005 and peaked in october 2005 before gradually subsiding. r was estimated to be 3.15 (3.14-3.16) and 27.21 (26.73-28 .05) for the two respective waves. the time series of monthly differences in male and female case data were found to be most significantly correlated at lag 0 (i.e., r > 0.7) with r = 0.906 and 0.804, respectively in each direction. the granger causality test indicated that the male time series caused the corresponding female time series with a lag of 2 months or less. conclusions: the modeling results revealed the presence of a small first wave in 2004, before an explosion of cases after may 2005. furthermore, a harm reduction program implemented in august 2005 contributed to the downturn in the epidemic after october. correlation results also suggest that the upsurge in male hiv cases led to the subsequent drastic surge in female cases. ß 2013 international society for infectious diseases. published by elsevier ltd. all rights reserved. hiv cases infected through idu diagnosed in 2003-2004 were infected with hiv subtype crf07_bc, which is totally different from the previously common subtype b and subtype crf01_ae in taiwan. as is typical of underreporting of hiv/aids among many hardto-count high-risk populations for hiv/aids, 9, 10 there is a significant discrepancy between reported and estimated hiv/aids cases in the idu group because of the difficulty reaching idus. in taiwan, where needle-sharing or apparatus-sharing behaviors have been found to be common among idus, the majority of newly diagnosed hiv/idus were detected through mandatory inmate screening upon entry to correctional facilities. however, mandatory hiv screening of persons under police custody due to violation of the narcotics control act since late 2004 could also have partially contributed to the sharp increase in detection. in response to the outbreak in idus, a harm reduction program, which involved a needle-syringe program (nsp) and substitution treatment, was implemented by the taiwanese government in august 2005 as an intervention to the rapidly increasing hiv epidemic since 2004. 4 there has been a steady drop in hiv incidence among idus in recent years, down from being the major mode of hiv transmission in taiwan in [2004] [2005] [2006] to below that of homosexual and heterosexual transmissions since 2007, but still significantly higher than its pre-2003 level. a recent molecular epidemiology study after the crf07_bc outbreak in taiwan concluded that while the percentage of crf07_bc among all hiv infections decreased from 2007 to 2009, the percentage of subtype b actually increased. 11 however, many questions remain regarding this sudden outbreak among the idu population. in this study the reported hiv/idu case data and a simple mathematical model, the richards model, [12] [13] [14] were used to investigate the temporal progression of this epidemic among idus in taiwan. in particular, the total case data are fit to the model, as well as the male and female case datasets separately, in order to ascertain the epidemic. correlation analysis was performed in an attempt to determine the relationship between the male and female idus. the data used here were extracted from the monthly reported hiv case data between april 2004 and march 2007, for a total of 36 months, made available by the taiwan centers for disease control and prevention (tcdc) on the tcdc website. 5 the data are provided for each risk group/factor and gender. however, the hiv/ idu case data by gender are only available after august 2004, the fifth month of the dataset. in what follows, for ease of illustration in the tables and figures, the months are numbered, namely, april 2004 is month 1 and march 2007 is month 36. the richards model, a logistic-type mathematical model was used in this study. the explicit solution of the richards model is of the form: where c(t) is the cumulative number of deaths at week t and the prime ' 0 ' denotes the time rate of change. k is the final outbreak size over a single wave of outbreak, r is the per capita growth rate of the cumulative case number, a is the exponent of deviation of the cumulative case curve, and t i is the turning point of the epidemic (which signifies the moment of upturn or downturn for the increase in the cumulative case number). the basic premise of the richards model is that the incidence curve of a single wave of infections consists of a single peak of high incidence, resulting in an s-shaped cumulative case curve and a single turning point (or the inflection point of the cumulative case curve) of the outbreak. this turning point t i , which is defined as the point in time at which the rate of accumulation changes from increasing to decreasing, or vice versa, can easily be pinpointed via the richards model. when more than one wave of infection occurs, a variation of the s-shaped richards model is proposed, 15 which makes the distinction between two types of turning points. other than the first turning point ending the initial exponential growth of the cumulative case number, a second type of turning point is present in a multi-wave epidemic where the growth rate of the cumulative case number begins to increase again, signifying the beginning of the next wave. for further illustrations, the readers are referred to hsieh and cheng 15 and hsieh and chen, 16 in which the incidence curves for the 2003 great toronto area severe acute respiratory syndrome (sars) and the 2007 taiwan dengue outbreaks containing two peaks (or two turning points of the first type) and one valley (or a turning point of second type) are investigated. for the computation of the basic reproduction number r 0 , the formula r 0 = exp (rt) was used, where t is the generation interval of the disease or the average interval from onset of one individual to the onset of his/her contacts. it has been shown mathematically 17 that, given the growth rate r, the expression r 0 = exp (rt) provides an upper bound for the basic reproduction number, regardless of the assumed distribution of the generation interval. we noted that in this instance, the estimate obtained is not the basic reproduction number, but the effective reproduction number r, since in taiwan hiv is endemic among the idu population and multiple intervention measures have already been in place for some years. the model parameters of epidemiological importance are k, r, and the turning point t i of the epidemic. the cumulative death data can be fitted to the richards model to obtain estimates of these model parameters, using any standard software with a least-squares approximation tool, e.g., sas, matlab, etc. more applications of the richards model on other infectious disease outbreaks such as dengue can also be found in hsieh and chen 16 and hsieh and stefan. 18 we first examined whether the times series were 'stationary', in order to avoid spurious regression, which could possibly result in a biased and inconsistent estimator. 19 a stationary time series means that its statistical characteristics do not change in time. in the event of a non-stationary time series, it can be suitably transformed to achieve stationarity. the augmented dickey-fuller (adf) test 19 was employed to verify if the random variables were indeed stationary series. three equations were used to test if the series process has a non-stationary character: 1. without drift and trend terms: 3. both drift and trend terms: the null hypothesis is non-stationary or unit root, i.e. to determine the correlation between the epidemic among the male and female idus through their time series of monthly case numbers, a distributed lag model (dlm) was employed to describe the relationship between the male and female time series. a dlm is a regression model that includes current and lagged values of one or more explanatory variables. this model allows the determination of what the effects are for a change in a time series. the resulting correlation coefficient, r, is a useful measure of linear strength between two random variables. the mathematical formula for computing r is: where n is the number of pairs of data. the value of r is such that à1 r + 1. the '+' and 'à' signs are used for positive linear correlations and negative linear correlations, respectively. if there is no linear correlation or a weak linear correlation, r is close to 0. a value near zero means that there is a random, nonlinear relationship between the two variables. 'jrj 0.4' means 'low correlation', '0.4 < jrj 0.7' means 'moderate correlation', and 'jrj > 0.7' means 'high correlation'. in other words, a correlation greater than 0.7 is generally described as strong, whereas a correlation less than 0.4 is generally described as weak. the granger approach 20 is used to ascertain how much of the current values of time series y can be explained by past values or some lagged values of time series y. the commonly used software eviews was developed originally by economists for use in economics applications, but can also be useful in other statistical applications. eviews version 5.0 (http://www.eviews.com/) was used to analyze the data. in general, it is better to use more lags rather than fewer lags, since the theory is couched in terms of the relevance of all past information. it is advisable to pick a lag length, l, which corresponds to the reasonable beliefs about the longest time over which one of the variables could help to predict the other. eviews performs bivariate regressions of the form: for all possible pairs of series in the group. the reported f-statistics are the wald statistics for the joint hypothesis: the null hypothesis is that series x does not granger-cause series y in the first regression and that y does not granger-cause x in the second regression. the monthly time series data of reported hiv cases for male idus, female idus, and all idus in taiwan were fit to the richards model as in figure 1 and table 1 the effective reproduction number r was computed for each wave. however, it is unclear what the generational interval is for hiv. it has been proposed that the rates of partner change for homosexuals and heterosexuals tend to be of the order of 1 year, 21 but it is unclear what the rate of needle-syringe sharing is among idus, [22] [23] [24] although it is most likely of shorter length than that of sexual transmission of hiv. due to the lack of a reliable estimate for the hiv generation time among idus in the literature, a generational interval of 5 or 6 months was assumed, based on an estimate of doubling time for aids cases among idus in the northeastern usa early in the epidemic. 22 it should be noted that the main purpose for estimating r in this study was to compare the transmissibility estimated using different datasets and to ascertain the relative temporal change in transmissibility that occurred in each wave of infection during the course of the epidemic. to table 2 , where the time series of monthly reported cases and the difference of two successive monthly reported cases were found to be stationary for both males and females. note that we use 'male' and 'female' to denote the respective time series of monthly reported male and female hiv cases, and '4male' and '4female' to denote the respective time series of differences of monthly male and female hiv cases. next, the correlation between the monthly reported case data (male and female) and monthly differences in case data (4male and 4female) were analyzed. the correlation coefficient r is a useful measure of the linear strength between two random variables. applying a univariate model of y = b 0 + bx t à lag + e t for 'x causes y' (or x ! y) with lag, male ! female and 4male ! 4female were found to be most significantly correlated (i.e., r > 0.7) with r = 0.906 and 0.804 with lag 0, respectively. the correlation plots for the correlation are given in figure 2 , which indicates the most significant correlations between the male reported cases and female reported cases, as well as their differences, are consistently at lag 0 (in red). the granger causality test was subsequently carried out between the time series of male and female and between the time series of 4male and 4female for time lags up to 5 months. test results, also given in table 3 with the causal direction for each pair indicated with an arrow, indicate that both male time series caused the corresponding female time series after a lag of 2 months. the timelines of the epidemic for all cases, as well as for the male and female case numbers, are illustrated in figure 3 , indicating good agreement among estimates of temporal progression of the epidemic using the three datasets, and pinpointing may 2005 as the month that separated the two waves obtained from all three datasets. it is further concluded that the turning points for the first of these two waves differ slightly at 16 17 .05), respectively, for the total, male, and female case data (see table 1 (18 + 4.19) , for all cases, males, and females, respectively. it is interesting to note that in a recent study, 25 phylogenetic tree analysis of 451 hiv-infected inmates with an idu history in taiwan was employed to demonstrate that there were two waves of hiv-1 crf07_bc infection from mainland china to taiwan. although no timeline of the two waves was available from the molecular study, it does corroborate our modeling results. the estimates for r indicate that the transmissibility of hiv among the idu population increased from the first wave to the second wave according to all three datasets, culminating in a peak around october 2005, when a downward trend ensued. it is interesting to note that the harm reduction program that was implemented by the taiwanese government in august 2005 could have impacted the downturn in case numbers after october, as revealed by our modeling results. however, only a trial harm reduction program, which included a needle-syringe program (nsp) and substitution treatment in four counties, was established at that time. after 1 year of the pilot study, data indicated that the hiv incidence in cities with an nsp decreased from 13.9 to 13.3 per 100 000 persons compared to an incidence increase from 11.5 to 15.3 per 100 000 persons in cities without an nsp. 26 subsequently, the harm reduction program was expanded to the whole of taiwan in july 2006. therefore, the country-wide downturn in case numbers after october 2005 may only be partially attributable to the harm reduction program. r for females was higher than that of males in the first wave, but lower in the second wave and ending earlier in june 2006, perhaps reflecting the more rapid initial increase in female incidence in the early stages of the epidemic. however, this drastic upsurge in female hiv-infected idus was relatively more difficult to sustain in the second wave, as indicated by the shorter length of this wave when compared to that of the males. therefore the epidemic impacted female idus more drastically initially, but the overall magnitude of infection was still less than that of the males, which was the group most affected by the epidemic. correlation analysis of the time series of male and female cases indicates that the outbreak among female idus was most likely driven by the infections among male idus, who were far more numerous at the beginning of the epidemic. in the granger causality test, the lag length corresponds to the longest time over which one of the variables could help to predict the other. therefore, the minimum p-value at a lag of 2 months for both the time series of case numbers and the first differences of the time series suggests that the strongest causality relationship, of male infections causing female infections, was within 2 months, a rather immediate relationship that led to the sudden upsurge in reported female hiv/idu cases shortly after the upsurge of the male idu cases in early 2004. it also indicates that there is likely some needle-sharing or apparatus-sharing among and between male and female idus, although one cannot rule out the possibility of sexual contact between the male and female idus, since one study 25 in taiwan found that 99.1% of the hiv-infected idus participating in the study were heterosexual. unfortunately no data on any relationships that might exist between the reported cases were available. the study further demonstrates how quickly a disease traditionally endemic in a male population can develop into an epidemic in the female population given appropriate circumstances; hence transmission across gender is an important aspect of disease surveillance. in summary, the abrupt outbreak among idus in taiwan in 2004-2007, which was caused by the recently introduced crf07_bc recombinant, led to two waves of infection with increasing transmissibility as measured by the effective reproduction number r during each wave, suggesting the presence of a small first wave in 2004 before the explosion of cases after may 2005. this further demonstrates the future potential of real-time modeling and analysis of disease data 27 as part of a disease surveillance system, which could conceivably detect and alert the authorities of a possible herald wave before the arrival of a major outbreak. the waves ended by march 2007, which could be attributable to a timely and effective harm reduction program implemented in august 2005; this has been essential in preventing further occurrences of wide-spread infections among idus in taiwan since 2007. furthermore, the infections among male idus led to the epidemic among the female idus, a population that had previously been mostly devoid of hiv infections. the limitation of this modeling study arises mainly from the nature of the hiv surveillance data, which typically consists of a longer period of time due to the long hiv incubation period, and hence is highly dependent on temporal changes in testing, reporting, and interventions over the years. in this study, the data that were used spanned a period of roughly 3 years, during which time the explosive outbreak among idus emerged; this subsequently led to interventions that included wider testing of idus in taiwan and the harm reduction program. moreover, while the simple mathematical model that was employed was able to reveal the temporal progression, culmination, and conclusion of the outbreak, it was unable to further pinpoint the exact impact of these intervention measures on the outbreak, which would require much more detailed data on the reported cases as well as a far more complicated mathematical model. hiv-1 crf07_bc infections, injecting drug users hiv-1 in taiwan molecular epidemiology of hiv-1 infection and full-length genomic analysis of circulating recombinant form 07_bc strains from injecting drug users in taiwan the changing epidemiology of prevalent diagnosed hiv infections in taiwan disease control and prevention. hiv/aids database timeline of the hiv epidemic among the idu population in taiwan diseases%20&%20prevention/issues%20of%20hiv-aids/statistics%20of%20hiv-aids/download%20hiv-aids%20data.htm a recent outbreak of human immunodeficiency virus type 1 infection in southern china was initiated by two highly homogeneous, geographically separated strains, circulating recombinant form ae and a novel bc recombinant asia and africa: on different trajectories? the lack of epidemiological link between the hiv type 1 infections in hong kong and mainland china empirical bayes approach to estimate the number of hiv-infected individuals in hidden and elusive populations ascertaining hiv underreporting in low prevalence countries using the approximate ratio of underreporting surveillance of hiv type 1 recent infection and molecular epidemiology among different risk behaviors between 2007 and 2009 after the hiv type 1 crf07_bc outbreak in taiwan a flexible growth function for empirical use severe acute respiratory syndrome epidemic in asia real-time forecast of multi-wave epidemic outbreaks turning points, reproduction number, and impact of climatological events on multi-wave dengue outbreaks how generation intervals shape the relationship between growth rates and reproductive numbers intervention measures, turning point, and reproduction number for dengue testing for unit roots in autoregressive moving average models of unknown order investigating causal relations by econometric models and crossspectral methods epidemiological parameters of hiv transmission needles that kill: modeling human immunodeficiency virus transmission via shared drug injection equipment in shooting galleries rm. drugs, sex and hiv: a mathematical model for new york city population dynamics of hiv-1 inferred from gene sequences molecular epidemiology of hiv-1 subtype b, crf01_ae, and crf07_bc infection among injection drug users in taiwan oral presentation epidemic modeling in real time: 2009 novel a (h1n1) influenza outbreak in canada yhh is supported by grants nsc 100-2314-b-039-028-my3 and 100-2115-m-039-002 from the national science council of taiwan. the author is grateful to the reviewers for their constructive and insightful comments, which significantly improved this manuscript.conflict of interest: no competing interest declared. key: cord-260518-mswb3q67 authors: zumla, alimuddin; dar, osman; kock, richard; muturi, matthew; ntoumi, francine; kaleebu, pontiano; eusebio, macete; mfinanga, sayoki; bates, matthew; mwaba, peter; ansumana, rashid; khan, mishal; alagaili, abdulaziz n.; cotten, matthew; azhar, esam i.; maeurer, markus; ippolito, giuseppe; petersen, eskild title: taking forward a ‘one health’ approach for turning the tide against the middle east respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential date: 2016-06-15 journal: int j infect dis doi: 10.1016/j.ijid.2016.06.012 sha: doc_id: 260518 cord_uid: mswb3q67 the appearance of novel pathogens of humans with epidemic potential and high mortality rates have threatened global health security for centuries. over the past few decades new zoonotic infectious diseases of humans caused by pathogens arising from animal reservoirs have included west nile virus, yellow fever virus, ebola virus, nipah virus, lassa fever virus, hanta virus, dengue fever virus, rift valley fever virus, crimean-congo haemorrhagic fever virus, severe acute respiratory syndrome coronavirus, highly pathogenic avian influenza viruses, middle east respiratory syndrome coronavirus, and zika virus. the recent ebola virus disease epidemic in west africa and the ongoing zika virus outbreak in south america highlight the urgent need for local, regional and international public health systems to be be more coordinated and better prepared. the one health concept focuses on the relationship and interconnectedness between humans, animals and the environment, and recognizes that the health and wellbeing of humans is intimately connected to the health of animals and their environment (and vice versa). critical to the establishment of a one health platform is the creation of a multidisciplinary team with a range of expertise including public health officers, physicians, veterinarians, animal husbandry specialists, agriculturalists, ecologists, vector biologists, viral phylogeneticists, and researchers to co-operate, collaborate to learn more about zoonotic spread between animals, humans and the environment and to monitor, respond to and prevent major outbreaks. we discuss the unique opportunities for middle eastern and african stakeholders to take leadership in building equitable and effective partnerships with all stakeholders involved in human and health systems to take forward a ‘one health’ approach to control such zoonotic pathogens with epidemic potential. benefit the large majority of affected people. some foreign aid workers and researchers were not familiar with local cultural and medical services norms and aroused local anxieties. 10 the evd epidemic highlighted the need for developing more comprehensive local, national, international, and global surveillance, as well as epidemic and outbreak preparedness response infrastructures. multiple animal, human, and environmental factors are obviously playing a critical role in the evolution, transmission, and pathogenesis of zoonotic pathogens, and these require urgent definition to enable appropriate interventions to be developed for optimal surveillance, detection, management, laboratory analysis, prevention, and control in both human and animal populations. an important need exists for establishing long-term, sustainable, trusting and meaningful and equitable collaborations between the animal, human, ecosystem, and environmental health sectors at the local, national, and international levels. these should include sustainable political and funder support for developing human and laboratory capacity and training that enables effective human-animal health cooperation leading to proactive surveillance, early detection of potential pandemic pathogens, and rapid initiation of public health prevention and control guidelines and interventions. whilst a long list of pathogens with epidemic potential are on the radar of the world health organization (who), 2 ideally 'prevention is better than cure' and new pathogens should be dealt with at the animal source, tackling the drivers and triggers of pathogen evolution and emergence. this requires close cooperation between human and animal health systems and an appreciation of human impacts on the environment at all levels and easy access to adequate laboratory facilities. on december 10, 2015 an expert panel convened by who prioritized a list of emerging pathogens ''considered likely to cause severe outbreaks in the near future, and for which no, or insufficient, preventive and curative solutions exist''. 11, 12 the list of the top 10 includes the new viral zoonotic pathogen of humans mers-cov, 13, 14 which was first isolated from a patient who died of a severe respiratory illness in a hospital in jeddah, saudi arabia in june 2012. 15 the emergence of mers-cov in 2012 15 was the second time (after sars-cov 16 ) that a highly pathogenic coronavirus of humans emerged in the 21 st century. 17 a strong link between human cases of mers-cov and dromedary camels has been established through several studies. [18] [19] [20] [21] [22] [23] [24] [25] [26] mers-cov is endemic in the camel populations of east africa and the middle east 21, 25, 26 and presents a constant threat to human health in both regions. retrospective studies using stored serum from different geographical locations have indicated that mers-cov has been circulating for several decades. 25 as of may 1, 2016, there have been 1733 laboratoryconfirmed cases of mers reported to the who, 27 with a mortality of 34% (628 cases died). whilst most mers cases have been reported from the middle east (a large proportion from saudi arabia), mers cases have been reported from 27 countries in all continents. 27 the who has held nine meetings of the emergency committee (ec) for mers-cov. 28 since evidence of sustained human-to-human transmission of mers-cov in the community is lacking, the who currently does not recommend travel restrictions to the middle east. however, mers-cov remains a major global public health threat with continuing reports of new human mers cases in saudi arabia, where millions of pilgrims from over 184 countries travel throughout the year. 29 furthermore, a more intensive farm-based camel livestock system has emerged and there is a large, wellestablished trade in camels between countries at the horn of africa and countries in the middle east. this has increased significantly, particularly following the lifting of the ban on live animal imports from somalia by saudi arabia in 2009/2010. somalia now exports some five million live animals every year to the gulf arab states (including 77 000 camels), making it the single biggest exporter of live animals in the world. the positive experience of reviving somalia's livestock export industry through increased investment in animal disease prevention and control strategies highlights how effective the 'one health' approach can be. most of the african countries do not have the resources, expertise, or capacity, including laboratory facilities, to have active surveillance for mers-cov in place. in light of this, the need for increased vigilance and watchful surveillance for mers-cov in sub-saharan africa has been highlighted previously. 30 such an initiative could be supported through investments by countries that import large numbers of camels and other livestock from the region. the epidemic potential of mers-cov was recently illustrated by a large outbreak in hospitals in seoul, the republic korea, in mid-2015: mers-cov was imported by a traveller to the middle east (an agriculture businessman), resulting in 184 mers cases with 33 deaths. 31 the first case was reported on may 20, 2015 and over the ensuing 3 weeks, the number of secondary, tertiary, and perhaps quaternary cases of mers from this single patient rose rapidly, resulting in the largest mers case cluster occurring outside the middle east. the unprecedented outbreak was attributed to poor infection control measures at the hospitals. 30 sequencing studies of the mers-cov isolate showed genetic recombination of mers-cov in the case exported from korea to china. 32 however, recombination is a frequent event in mers-cov and the korean outbreak is unlikely to represent a special form of the virus. nonetheless, the potential evolution of mers-cov into a more virulent form needs to be monitored closely. research on sequencing seems to have stagnated and there have been no further sequences published from new human mers cases reported from the middle east. furthermore, the genetic evolution of mers-cov strains infecting humans over the past year remains unknown. there is an urgent need for more sequencing studies on mers-cov evolution in camels and humans, with the development of appropriate local capacity for these studies. the kingdom of saudi arabia has kept proactive watchful mers-cov surveillance with regular reports to the who of mers-cov cases. 33 the who and ministries of health of middle eastern countries continue watchful surveillance of the mers-cov situation, and the watchful anticipation is that mers-cov may disappear with time like sars-cov. however, with the continuing, regular reports of community cases of mers-cov from saudi arabia, 27 there are no signs of this happening in the near future and lessons must be learnt from the korean outbreak. 34 whilst there is a growing camel livestock industry in the region, elimination of the virus is unlikely in the short term. several animal, human, and environmental factors are obviously playing a critical role in the repeated movement of mers-cov from camels to humans. the disease ecology remains largely unknown. urgent definition is required to enable appropriate interventions to be developed for optimal surveillance, laboratory detection, management, prevention, and control in both human and animal populations. whilst several ad hoc research studies have been conducted and findings published over the past 4 years, more comprehensive investments in tackling mers-cov have not been forthcoming. there remain huge knowledge gaps on mers-cov. much of the information that we have about the source of mers-cov infections is based on small local studies and it is difficult to develop general country-wide policies without a clear understanding of the zoonotic problem. questions remain, for example are new local mers outbreaks in saudi arabia always seeded by the same type of human exposure to camels? are there particular regions of africa that provide infected camels to saudi arabia? or is there a general risk from all regions? is there a way to efficiently control the entry of infected camels? are animal vaccination strategies economically viable given the large number of imported animals and the frequency of the infection? a clear policy in which full virus genome sequences are generated from every outbreak in the country and in which virus from subsets of imported camels is routinely screened and sequenced after 2 years, would provide incredibly useful information about the transmission patterns of the virus and how to stop it. certainly the resources and expertise to perform this sequence monitoring are available and only governmental support is needed to run such a survey. the cost of such a survey would be far less than the management costs and grief associated with a single hospital outbreak. numerous priority research questions regarding mers-cov (basic science, epidemiology, management, and development of new diagnostics, biomarkers, treatments, and vaccines) in both humans and camels, highlighted 2 years ago by the who mers expert groups 35 and by others, 36 remain unanswered. these have again been raised recently, highlighted by calls from saudi arabian health care staff and scientists 37, 38 and by yet another who mers expert group, which has defined a ''roadmap for research and product development against mers-cov''. 39 in 2000 the who set up the global outbreak alert and response network (goarn) 40 for better coordination of surveillance efforts across the globe. it networks 150 institutions and partner agencies, with cooperation with other agencies such as public health england and the us centers for disease control and prevention (cdc) and consortia such as the international severe acute respiratory and emerging infection consortium (isaric). 41 recent consortia such as glopid-r aim to bring together research funding organizations on a global scale to facilitate an effective research response within 48 h of a significant outbreak of a new or re-emerging infectious disease with pandemic potential. 42 the past 4 years has seen outbreaks of ebola virus, zkv, and mers-cov, [2] [3] [4] 13 which indicate that the global community needs to seriously reflect on what is critically missing from current political, scientific, and public health agendas, and how to delineate what is required at the national, regional, and global levels to prevent future epidemics. the factors and operating conditions that promote the emergence and geographical spread of zoonoses are complex and may be related to a single event or chain of multiple events influenced by the genetic evolution of the pathogen, environmental and climate changes, anthropological and demographic changes, and movement and behaviour of humans, animals, and vectors. with animal, human, and environmental factors playing a critical role in its evolution, mers-cov requires more close collaboration between human and animal health systems and university academics to reduce the risk of pandemic spread. 43 moreover, a better understanding of the agricultural dynamics involved in its persistence and spread in camels and studies on interactions between hosts in the environment are urgently needed. the intermittent detection and reporting of mers cases in the community and sporadic nosocomial mers-cov outbreaks will require a more coordinated response plan to study clinical cases, conduct translational basic science and clinical trials research, and perform longitudinal sequencing studies from human and camel mers-cov isolates. a more collaborative mers-cov response plan is required to better define mers-cov epidemiology, transmission dynamics, molecular evolution, laboratory capacity, optimal treatment and prevention measures, and development of vaccines for humans and camels. 44 a better understanding of the prevailing disease ecology and investigations into the dynamics of infectious agents in wildlife could act as a better means of preventing outbreaks in livestock and people at source. the 'one health' concept is an important concept that focuses on the relationship and interconnections between humans, animals, and the environment, and recognizes that the health and wellbeing of humans is intimately linked to the health of animals and their environment (and vice versa). [45] [46] [47] [48] [49] a balanced ecological approach improves understanding of the true threat of novel pathogens and helps to avoid costly, poor, and inappropriate responses to new diseases. in many cases, solutions can be found through altered development pathways and are not inevitably requiring of costly, unsustainable technical and pharmaceutical interventions. thus it is ideally suited to the mers-cov situation in which camels, humans, and environmental factors are central to its persistence and evolution. since the kingdom of saudi arabia is host to millions of pilgrims each year travelling from all continents, 29 tackling the threat of mers and other infectious diseases with epidemic potential will require enhanced closer cooperation between those who provide human health, animal health, and environmental health services, locally, nationally, regionally, and internationally: the middle eastern, european, african, asian, and american governments, veterinary groups, the who, the food and agriculture organization (fao), the african union, the united nations international children's emergency fund (unicef), the world bank, office international des epizooties (oie), cdc, public health england, the newly formed africa cdc, and funding agencies among others. they should now demonstrate increased commitment towards local, national, and global multidisciplinary collaborative efforts to secure optimal health for people, animals, and the environment. global efforts need to be focused on establishing the capability for and strengthening of surveillance systems in developing countries, particularly in africa where emerging and re-emerging zoonoses are a recurrent problem. a prime emphasis should be on developing awareness and response capacity in all countries and on promoting interdisciplinary collaboration and coordination. critical to the establishment of a well-functioning 'one health' platform is the creation of a multidisciplinary team with a range of expertise, including public health officers, physicians, veterinarians, animal husbandry specialists, agriculturalists, ecologists, vector biologists, viral geneticists, and researchers, with easy access to adequate laboratory facilities, who will collaborate in order to learn more about zoonotic spread between animals, humans, and the environment and to monitor, respond to, and prevent major outbreaks. there is an urgent and critical need to build a sustainable public health programme and rapid response capability for outbreaks of zoonotic pathogens in the middle east and in low-income countries, especially in africa. importantly there is a need for capacity development programmes designed to strengthen research training and build career pathways for the best and brightest post-doctoral researchers, including phd and masters students working at the interface of humans, animals, and environment. these should include national or regional laboratory facilities, as surveillance requires laboratory support to be meaningful. the development of human and animal health research leaders will create a critical mass of local research capacity and the development of self-funding research environments in african universities and research institutes. this capacity growth could be facilitated through the further development and support of a geographical network of equitable and enduring south-south and north-south partnerships. 9. need for more effective political and scientific engagement to eradicate the threat of mers-cov and other zoonotic diseases the persistence of mers-cov 4 years since its first discovery has created major opportunities for each of the middle eastern and african countries to take leadership of the 'one health' approach with a view to bringing this under regional and global umbrellas, to tackle new emerging and re-emerging infectious diseases with epidemic potential. this will also devolve current dominance of the global health agenda by western groups and consortia and allow equitable partnerships to be established with long-term sustainability. the past year has seen some progress in research into mers-cov, but there remains a need for a more effective, coordinated, and multidisciplinary 'one health' consortium to take forward mers-cov research on priority areas already defined by saudi scientists 37, 38 and the who mers committee. 39 the establishment of regional 'one health' centres of excellence in the middle east (under the league of arab states) and at specific geographical locations in west, central, east, and southern africa could make an important difference in mitigating the risks and factors that pose a risk to both human and animal health. furthermore, any operational plan developed will contribute to strengthening the sentinel surveillance systems in sub-saharan africa in the preparedness and response to potential outbreaks. regional centres should be sufficiently empowered to manage the spectrum of 'one health' approaches to zoonotic disease control in humans and animals, from behaviour change and social interventions for prevention to surveillance of infections and antimicrobial resistance, and preparedness and response to outbreaks. a model for the major syndromes (respiratory, neurological, haemorrhagic, gastro-enteric, and sepsis-like presentations) should be developed so that clinical protocols may be adapted rapidly for any major outbreak during mass gatherings. this should include the development and introduction of innovative and smart platforms for data sourcing, sample collection, and analysis, in order to give clinicians and public health workers continuously updated information on which clinical decisions may be based. there is a pressing need to develop and strengthen the national ethics and medicines regulatory frameworks in sub-saharan africa in order to strike a balance between the public health interest, the interests of the pharmaceutical industry, and ethical values. parallel initiatives across africa and the tropics could be harmonized to create regional networks that can serve as a repository for expert 'one health' advice on agriculture, sustainable livestock, and the links to human development. there are several ongoing important initiatives on developing 'rapid response' and broader 'one health' capacity development groups in europe, asia, and the americas to assist in the surveillance and response to emerging infectious disease threats. the public health systems of west african countries failed with the ebola epidemic, and the response from the who and the international community was very slow and uncoordinated. this led to thousands of people, including over 500 health care workers, losing their lives. the factors governing the appearance and disappearance of new coronaviruses affecting humans are complex and it has been over 4 years since the first patient died of mers-cov. mers cases continue to be reported throughout the year from the middle east. there is a large mers-cov camel reservoir and there is no specific treatment or vaccine. the precise pathway from infected camel to the recurring mers hospital outbreaks needs to be understood in order to devise effective control measures. with 10 million people visiting saudi arabia every year for umrah and/or hajj and the increasing importation of live animals from sub-saharan africa, the potential risk of global spread will be everpresent, especially if mutations or recombinations in mers-cov occur. a major 'one health' initiative to tackle mers-cov at source in animal populations is thus required. 50 middle eastern and african governments should now work more closely together and increase collaborative efforts with international partners and global public health authorities if we are to prevent yet another global zoonotic pandemic. conflict of interest: all authors have a specific interest in 'one health'. the authors declare no conflicts of interest. there was no financial support. emerging and re-emerging infectious threats in the 21st century world health organization. ebola virus disease outbreak world health organization. zika virus be prepared: europe needs ebola outbreak consortium ethics for pandemics beyond influenza: ebola, drug-resistant tuberculosis, and anticipating future ethical challenges in pandemic preparedness and response ebola: missed opportunities for europe-africa research rapid spread of zika virus in the americas-implications for public health preparedness for mass gatherings at the 2016 brazil olympic games lessons from the ebola outbreak: action items for emerging infectious disease preparedness and response challenges in controlling the ebola outbreak in two prefectures in guinea: why did communities continue to resist? world health organization. who publishes list of top emerging diseases likely to cause major epidemics world health organization. a research and development blueprint for action to prevent epidemics 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humans advancing priority research on the middle east respiratory syndrome coronavirus in riyadh, ksa knowledge gaps in therapeutic and non-therapeutic research on the middle east respiratory syndrome world health organization. a roadmap for research and product development against middle east respiratory syndrome-coronavirus (mers-cov) international severe acute respiratory and emerging infection consortium. the website for the international severe acute respiratory and emerging infection consortium (isaric) global research collaboration for infectious disease preparedness website emerging infectious diseases and pandemic potential: status quo and reducing risk of global spread development of medical countermeasures to middle east respiratory syndrome coronavirus what is one health? one health global network one health: a new professional imperative. one health initiative task force one world, one health. oie-world organisation for animal health sharing responsibilities and coordinating global activities to address health risks at the animal-human-ecosystems interfaces. a tripartite concept note international organization for standardization. who develops iso standards. geneva: who towards a one health approach to controlling zoonotic diseases key: cord-304743-0bsdahh6 authors: kortepeter, mark g; dierberg, kerry; shenoy, erica s; cieslak, theodore j; bhadelia, nahid; davey, richard t; evans, jared d; frank, maria g; grein, jonathan; kraft, colleen s; kratochvil, chris j; martins, karen; mclellan, susan; measer, greg; mehta, aneesh k; raabe, vanessa; risi, george; sauer, lauren; uyeki, timothy title: marburg virus disease: a summary for clinicians date: 2020-08-03 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.042 sha: doc_id: 304743 cord_uid: 0bsdahh6 abstract objectives this article is a summary of countermeasures for marburg virus disease focusing on pathogenesis, clinical features, and diagnostics, with an emphasis on therapies and vaccines that have demonstrated potential for use in an emergency situation, through their evaluation in nonhuman primates (nhps) and/or in humans. methods a standardized literature review was conducted on vaccines and treatments for each pathogen, with a focus on human and nonhuman primate data published in the last five years. more detail on the methods used are summarized in a companion methods paper. results we identified six treatments and four vaccine platforms that have demonstrated potential benefit for treating or preventing infection in humans, through their efficacy in nhps. conclusion we provide succinct summaries of marburg countermeasures to give the busy clinician a head start in reviewing the literature if faced with a patient with marburg virus disease. we also provide links to other authoritative sources of information. this is the first in a planned series on the management of highly hazardous communicable pathogens that may warrant specialized infection control measures and lack frankfurt, germany and belgrade, yugoslavia, as well as a subsequent outbreak among three travelers cared for in south africa. (martini, 1971; gear et al, 1975) following the incubation period, patients usually become ill abruptly, with non-specific symptoms such as fever, chills, headache, odynophagia, myalgia, vomiting, and diarrhea. early cases may be missed, owing to similarities with more common infections, such as malaria, typhoid, or rickettsial illness. rash is a common feature early in mvd, and is described as non-pruritic, erythematous, and maculopapular. it may begin focally, then become diffuse and confluent. as noted during the original outbreak, "it began between the fifth and seventh day at the buttocks, trunk, and outside j o u r n a l p r e -p r o o f of both upper arms as a distinctly marked, pin-sized red papula around the hair roots," which lasted up to 24 hours, then developed into a maculo-papular rash, which later coalesced. (martini, 1971 ) conjunctival injection may also occur early. during mvd, wide swings of body temperature have been noted, encompassing hyperand hypo-pyrexia. in the original outbreak, tachycardia corresponding to temperature elevation was only seen in fatal cases. lab abnormalities include leukopenia and lymphopenia, hypokalemia, normal to elevated levels of amylase, thrombocytopenia, and elevated liver enzymes. as illness progresses, elevations in prothrombin time and partial thromboplastin time, as well as clinical bleeding, may occur. patients may develop multiple foci of mucosal hemorrhage, typically in the conjunctivae, along with easy bruising or persistent bleeding from venipuncture sites. renal function may be normal initially, although by the end of the first week of illness, renal function is often impaired and dialysis may be required. severe cases progress from prostration and obtundation to hypotension, shock, and multi-organ failure. in the west african outbreak of evd, significant gastrointestinal disease was described, with vomiting and diarrhea leading to volume loss, acid base disturbances, and electrolyte imbalances. marburg haemorrhagic fever in returning travellers: an overview aimed at clinicians efficacy of favipiravir (t-705) in nonhuman primates infected with ebola virus or marburg virus remdesivir for the treatment of covid-19 -preliminary report serosurvey on household contacts of marburg hemorrhagic fever patients forty-five years of marburg virus research rational approach to disinfection and sterilization: guideline for disinfection and sterilization in healthcare facilities mva-bn®-filo and ad26.zebov vaccines in healthy volunteers persistent marburg virus infection in the testes of nonhuman primate survivors post-exposure treatments for ebola and marburg virus infections postexposure protection against marburg haemorrhagic fever with recombinant vesicular stomatitis virus vectors in non-human primates: an efficacy assessment controlled trial of ebola virus disease therapeutics how to treat ebola virus infections? a lesson from the field postexposure antibody prophylaxis protects nonhuman primates from filovirus disease progress in filovirus vaccine development: evaluating the potential for clinical use shifting the paradigm -applying universal standards of care to ebola virus disease outbreak of marburg virus disease in johnannesburg recombinant adenovirus serotype 26 (ad26) and ad35 vaccine vectors bypass immunity to ad5 and protect nonhuman primates against ebolavirus challenge vector choice determines immunogenicity and potency of genetic vaccines against angola marburg virus in nonhuman primates vesicular stomatitis virus-based vaccines protect nonhuman primates against aerosol challenge with ebola and marburg viruses. vaccine single-injection vaccine protects nonhuman primates against infection with marburg virus and three species of ebola virus postexposure treatment of marburg virus infections for marburg virus in nonhuman primates and humans safety and pharmacokinetic profiles of phosphorodiamidate morpholino oligomers with activity against ebola virus and marburg virus: results of two single-ascending-dose studies efficacy and effectiveness of an rvsv-vectored vaccine in preventing ebola virus disease: final results from the guinea ring vaccination, open-label, cluster-randomised trial (ebola ça suffit!) a polymorphism within the internal fusion loop of the ebola virus glycoprotein modulates host cell entry discovery and early development of avi-7537 and avi-7288 for the treatment of ebola virus and marburg virus infections late ebola virus relapse causing meningoencephalitis: a case report first newborn baby to receive experimental therapies survives ebola virus disease live attenuated recombinant vaccine protects nonhuman primates against ebola and marburg viruses laboratory findings, compassionate use of favipiravir, and outcome in patients with ebola virus disease, guinea, 2015-a retrospective observational study basic clinical and laboratory features of human filoviral fever uveal involvement in marburg virus disease current progress of dna vaccine studies in humans a dna vaccine for ebola virus is safe and immunogenic in a phase i clinical trial marburg virus disease. clinical syndrome marburg virus disease safety and immunogenicity of novel adenovirus type 26-and modified vaccinia ankara-vectored ebola j o u r n a l p r e -p r o o f vaccines: a randomized clinical trial durability of a vesicular stomatitis virus-based marburg virus vaccine in nonhuman primates therapeutic treatment of marburg and ravn virus infection in honhuman primates with a human monoclonal antibody controlled trial of ebola virus disease therapeutics recent advances in marburgvirus research calculation of incubation period and serial interval from multiple outbreaks of marburg virus disease online ahead of print ebola and marburg virus vaccines comparison of individual and combination dna vaccines for b. anthracis, ebola virus, marburg virus and venezuelan equine encephalitis virus ebola and marburg hemorrhagic fever clinical illness and outcomes in patients with ebola in sierra leone experimental treatment with favipiravir for ebola virus disease (the jiki trial): a historically controlled, single-arm proof-of-concept trial in guinea interferon-beta therapy prolongs survival in rhesus macaque models of ebola and marburg hemorrhagic fever chimpanzee adenovirus vaccine generates acute and durable protective immunity against ebolavirus challenge clinical course and prognosis of marburg virus (''green monkey'') disease monovalent viruslike particle vaccine protects guinea pigs and nonhuman primates against infection with multiple marburg viruses vaccine to confer to nonhuman primates complete protection against multistrain ebola and marburg virus infections marburg virus infection in nonhuman primates: therapeutic treatment by lipid-encapsulated sirna protection against lethal marburg virus infection mediated by lipid encapsulated small interfering rna advances in virus-like particle vaccines for filoviruses delayed time to treatment of an antisense morpholino oligomer is effective against lethal marburg virus infection in cynomolgus macaques protection against filovirus diseases by a novel broad-spectrum nucleoside analogue bcx4430 ebola virus disease among children in west africa postexposure efficacy of recombinant vesicular stomatitis virus vectors against high and low doses of marburg virus variant angola in nonhuman primates key: cord-255901-nl9k8uwd authors: barasheed, osamah; alfelali, mohammad; mushta, sami; bokhary, hamid; alshehri, jassir; attar, ammar a.; booy, robert; rashid, harunor title: uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review date: 2016-03-29 journal: int j infect dis doi: 10.1016/j.ijid.2016.03.023 sha: doc_id: 255901 cord_uid: nl9k8uwd objectives: the risk of acquisition and transmission of respiratory infections is high among attendees of mass gatherings (mgs). currently used interventions have limitations yet the role of facemask in preventing those infections at mg has not been systematically reviewed. we have conducted a systematic review to synthesise evidence about the uptake and effectiveness of facemask against respiratory infections in mgs. methods: a comprehensive literature search was conducted according to the preferred reporting items for systematic reviews and meta-analyses (prisma) guidelines using major electronic databases such as, medline, embase, scopus and cinahl. results: of 25 studies included, the pooled sample size was 12710 participants from 55 countries aged 11 to 89 years, 37% were female. the overall uptake of facemask ranged from 0.02% to 92.8% with an average of about 50%. only 13 studies examined the effectiveness of facemask, and their pooled estimate revealed significant protectiveness against respiratory infections (relative risk [rr] = 0.89, 95% ci: 0.84-0.94, p < 0.01), but the study end points varied widely. conclusion: a modest proportion of attendees of mgs use facemask, the practice is more widespread among health care workers. facemask use seems to be beneficial against certain respiratory infections at mgs but its effectiveness against specific infection remains unproven. the risk of acquisition and transmission of respiratory infections amplifies at mass gatherings (mgs) straining healthcare of the host country. for instance, in hajj, one of the largest annual mg events in the world, more than 2 million people attend each year in makkah, and over 90% suffer from at least one respiratory symptom, the risk of viral respiratory infections increases several folds and more severe respiratory infections such as pneumonia are the leading causes of hospital admission. [1] [2] [3] likewise, a number of influenza outbreaks were reported during the world youth day 2008, a large catholic gathering in sydney. 4 mgs are also linked to globalisation of various infections. for instance, the iztapalapa play passion, a religious festival in mexico, was believed to spark the outbreak of swine flu leading to its accelerated dissemination across the world. 5 therefore, international public health agencies, including world health organization (who), have issued guidelines on mass gathering preparedness to minimise the possible risks. 6 from a public health perspective, one of the key concerns is to prevent global spread of respiratory infections during mgs. interventions like vaccinations against viral and bacterial respiratory infections, anti-influenza prophylaxis and hand hygiene are considered as preventive measures but the measures have limitations. for instance, vaccinations against respiratory infections, such as influenza, are recommended for travellers to mgs such as hajj, 7 and even though a recent systematic review generally supports its effectiveness against laboratory-confirmed influenza at hajj, 8 frequent mismatch between vaccine strains and circulating strains is an important concern. 9 soaring antiviral resistance against both adamantanes and neuraminidase inhibitors is an issue that limits their widespread use in mgs. 4, 10 similarly, while hand hygiene has been recommended as a protective measure for attendees of mgs, its effectiveness is not fully evaluated in a mass gathering setting and the efficacy is debatable. 11 therefore, the role of another protective measure, facemask, should be explored in the prevention of respiratory infections. 12 facemask is believed to have a protective role in preventing nosocomial infections since the time of spanish influenza. 13 several studies have assessed the usefulness of facemask in household, community and healthcare settings, the findings of which have been summarised in a few reviews. [14] [15] [16] noticeable disparities of facemask effectiveness between these studies were observed. studies conducted in community or health care settings found facemasks to be generally effective against influenza-like illness (ili) or even against severe acute respiratory syndrome (sars) but its effectiveness against respiratory infections at mgs remains unknown. 15, 17 a review of non-pharmaceutical interventions against respiratory tract infections among hajj pilgrims presented data on the uptake of facemask and acknowledged that compliance was generally poor, but did not evaluate its effectiveness during hajj. 11 subsequently, further data on the uptake and effectiveness have become available, especially from a pilot randomised controlled trial (rct). 18 the aim of this systematic review is to explore the uptake and effectiveness of facemask against respiratory infections in mgs. studies were identified through searching electronic databases including; medline (pubmed and ovid), embase, scopus and cinahl from database inception to february 8, 2016. we used a combination of mesh terms and text words including: 'crowding' or 'mass gathering' or 'large event' or 'group assembly' or 'holiday' or 'travel' or 'sport' or 'olympic' or 'fifa' or 'festival' or 'hajj' (also alternative spelling 'hadj' or 'haj') or 'pilgrimage' and 'mask' or 'facemask' or 'surgical mask' or 'medical mask' or 'simple mask' and 'infection' or 'respiratory tract diseases' or 'disease outbreaks' or 'infectious disease' or 'respiratory tract infections' or 'influenza' or 'pneumonia'. additionally, an online search of pertinent epidemiology journals, including those not indexed in the mentioned databases (e.g. saudi epidemiology bulletin) was carried out through free hand google engine search. finally, manual search was performed reviewing reference lists of included studies to identify additional potentially relevant studies. the search result was presented according to the preferred reporting items for systematic reviews and meta-analyses (prisma) guidelines ( figure 1 ). 19 in the first phase, three authors (ob, sm and hb) identified the potential titles, and sifted the titles and abstracts against the inclusion criteria. titles of all studies published in english language and reported the use or effectiveness of facemask against respiratory infections in mgs were preliminarily included. studies that dealt with attendees of mgs of any age, gender and country were considered for inclusion. at the end of the screening phase, full texts of potentially relevant studies were retrieved for detailed study. finally studies that met the inclusion criteria were included for data synthesis. duplicates were excluded. five authors (ob, ma, hb, sm and ja) independently extracted the data from each study into a data extraction sheet which was divided in two sections, 'facemask uptake' and 'facemask effectiveness' and five authors subsequently cross-checked the entries (ob, aa, hb, sm and ja),while a sixth author (hr) arbitrated when a discrepancy occurred. the following data were abstracted in each extraction sheet: study design, year of conducting the study, sample size, country of origin, age, gender, diagnostic method used, definitions of study end point, and history of participants' chronic diseases, if available. the quality of the included studies were categorised according to a modified ranking criteria based on oxford evidence based medicine (http://www.cebm.net/) into groups (e.g., a, b, c, d) where a was for rcts of adequate sample size, b for observational studies of adequate sample size with good quality or pilot rcts or non-randomised trial, c for observational studies of inadequate sample size or of poor quality, and d for cases series, such as focus groups or qualitative surveys. the search results are summarised in figure 1 the study sample sizes varied widely ranging from 10 to 1717 participants. the included studies contained the pooled data of 12710 participants aged between 11 and 89 years (mean age ranged from 33.5 to 61.7 years in individual studies). about 37% of the pooled samples were females, in individual studies the proportion of females ranged from 10% to 63%. excluding three studies, which involved hcws deployed at hajj, [23] [24] [25] all other included studies involved hajj pilgrims. the origin of the participants varied depending on the study, seven studies included multinational participants, while the other 18 were exclusive to participants from a single country of origin; seven out of 18 (38.9%) were from saudi arabia, 20,23-28 according to study types 11 out of 25 were cohort studies, 1,2,22-24,28-33 another 11 cross-sectional studies, 21,25-27,34-40 two trials (not necessarily rcts) 18, 20 and one case-series conducted as a qualitative study 41 (table 1) . the median uptake of facemask in pooled sample was 53.5%. the lowest reported uptake was 0.02% by elachola et al. among pilgrims in a unique study that involved quantification of facemasks through photo frames from surveillance camera during the hajj in 2013, therefor it is considered as an outlier. 21 the highest uptake was 92.8% observed by al-asmary et al. among health care workers during hajj in 2005. 24 excluding these two studies (elachola et al 21 and al-asmary et al 24 ) , uptake rate among pilgrims has remained generally steady with gradual increase from 24% in 1999 to 64% in 2014 with minor fluctuations (figure 2 ). studies involving hcws reported an uptake from 50% in 2009 to 92.8% in 2005. according to the pilgrims' country of origin, malaysian pilgrims were noticed to be most compliant to using facemasks (70.9%), 37,40 followed by french (60.5%) 1,2,32,33 and iranians (60%) 31 (table 1) . only three studies, all involving australian pilgrims, evaluated the reasons of compliance (or non-compliance) of using facemask during hajj. 18, 29, 41 the most reported reasons for wearing facemask were to avoid transmission of infectious organisms and protection from air pollution. 29 however, discomfort and difficulty in breathing were the most reported reasons for not wearing facemask. 18,41 thirteen studies investigated the effectiveness/efficacy of facemask against respiratory infections, but the endpoints varied very widely. most of these studies (9 out of 13) used a combination of respiratory symptoms (syndromic) as endpoints with varying definitions. for instance, acute respiratory infections (ari) was used as an endpoint in three studies, 20,24,28 ili in two, 18, 37 upper respiratory tract infection (urti) in two, 22, 26 respiratory illness in two 30, 40 and respiratory tract infections in one. 31 however a couple of studies used only one respiratory symptom as an endpoint: fever 39 and cough. 32 only one study established laboratory-proven viral infections 25 as an endpoint. definitions for the endpoints are detailed in table 2 . in regards to the effectiveness of facemask, four out of thirteen studies demonstrated significant effect against respiratory infections, 18, 20, 22, 28 two others showed some effect but did not reach statistical significance. 25, 26 one study assessed its effectiveness against fever but ruled out its protectiveness, 39 and the other six studies did not show effectiveness but results were not statistically significant. 24, [30] [31] [32] 37, 40 the pooled data from all studies revealed significant protectiveness of facemasks against respiratory infections in general at hajj (relative risk [rr] = 0.89, 95% ci: 0.84-0.94, p < 0.01) ( table 2) . according to the ranking system we used, most of the studies were of average quality (c) whereas two studies were ranked above average (b): a pilot rct 18 and a large cross-sectional study, 26 the other seven studies were of below average quality (d) either because of small sample size or poor study quality (table 1) . this systematic review shows that the use of facemask among the attendees of mgs remains essentially unchanged for decades although exceptionally in one study a very high uptake (about 93%) 24 or a very low uptake rate (0.02%) 21 has been reported but such variability can be explained by their unique study designs or population characteristics. the pooled data of this systematic review suggest that facemask is generally effective against respiratory infections at hajj, however the endpoints varied widely. the uptake of facemask among hcws deployed at hajj was generally higher than that among ordinary hajj pilgrims with average compliance among hcws being 72% compared to 46% among pilgrims. this finding is similar to what have been found in other studies that examined the uptake of facemask in other settings such as health care and community settings. for instance, the uptake of facemask among hcws in several studies ranged from 56.6% to 84.3% (average 70.7%). [42] [43] [44] [45] on the other hand, the uptake of facemask among ordinary population in diverse household and community settings ranged from 38% to 80.7% (average 55%). [46] [47] [48] [49] [50] [51] [52] this could be explained by several individual or organisational factors. for example, hcws have firsthand knowledge about the risk of respiratory infections and the role of preventive measurements in hajj. 25 similarly, studies in non-mgs settings showed a positive relationship between hcws' knowledge about the risk of infectious diseases and their compliance to preventive measures including the use of facemask. [53] [54] [55] organisational factors such as ready availability of facemask in health care settings, proper training programs and supportive policy of health care system could have played an important role in improving the compliance of hcws to facemask use. [54] [55] [56] [57] on the other hand, limited studies explored these individual and organisational factors among hajj pilgrims. a few studies showed that providing educational session on protective measures against respiratory infections (including facemask) before hajj was associated with significantly higher uptake of facemasks among pilgrims. 18, 20, 27, 36, 38 moreover, adequate accessibility and availability of facemask during hajj may enhance the compliance of pilgrims. abdin et al and barasheed et al revealed a higher uptake of facemask among groups who were provided with sufficient quantity of free facemask (81.3% versus 33.6%, p < 0.01, and 76% versus 12%, p < 0.01, respectively). 18, 20 however, reasons for not using facemask during hajj have not been explored adequately. while use of facemask at hajj has been officially recommended by saudi ministry of health since 2014, it is too early to have a significant impact on pilgrims' practice of facemask use. 58 although hajj took place in different seasons (spring, winter and autumn), the uptake of facemask among hajj pilgrims during the last decade remained generally stable (figure 2) . findings also showed that there was no significant change in facemask uptake among hajj pilgrims during the course of influenza a (h1n1) pandemic outburst in 2009, and the middle east respiratory syndrome corona virus (mers-cov) outbreak since 2012. this does not concur with what has been reported in published studies involving the members of general public over the several outbreaks of respiratory infections in non-mg settings. [59] [60] [61] [62] [63] [64] those studies showed an increase in facemask use during the outbreaks due to participants' perceived threat of infection. poor awareness among many pilgrims of contemporary outbreaks might explain why their uptake of facemask did not increase even during an ongoing outbreak. [65] [66] [67] interestingly, pilgrims of asian origin (e.g. malaysians) had higher facemask uptake compared to pilgrims from other regions. 37, 40 a polling study that evaluated the uptake of non-pharmaceutical measures during the pandemic influenza a (h1n1) of 2009 found that participants of asian origin (e.g. japan) had the higher facemask uptake (71%) compared to the uptake of participants of western or latin american origin. 68 presence of several peaks of influenza seasons in some asian countries, overcrowding, dense smog and air pollution in many cities may explain the higher uptake of facemask among people from asian countries; 69,70 additionally, cultural acceptance practice of the population around facemask while in public may make a difference. 68 focused studies are required to investigate factors influencing facemask compliance among attendees of hajj and other mgs. in this systematic review, pooled data of facemask effectiveness showed that participants who used facemask during hajj are about 20% less likely to suffer from respiratory infections compared to those who do not use it. this effectiveness of facemask is inconclusive due to great heterogeneity in study questions, assessment methods, study designs and qualities, and endpoints. in regards to the research questions, three out of 13 studies investigated facemask effectiveness as the primary research objective: all three studies yielded significant results; whereas only one out of the other 10 studies that assessed facemask as a secondary or indirect outcome, yielded significant results. further, there was great heterogeneity in how the frequency and duration of facemask use were assessed. although, most of the studies used a self-reported questionnaire to quantify facemask uptake among participants, the qualitative descriptive terms that the studies used (e.g. ''always'', ''mostly'', ''sometimes'' or ''never'') may have introduced subjective bias, since qualitative description varies depending on participants' perception about the frequency and duration of use. however, only one study used measurable criteria in their questionnaires to quantify the number of facemasks used including the duration (in hours) and frequency of use, finding that using facemask more than eight hours per day was associated with significant decrease in ili symptoms among hajj pilgrims. 18 using surveys with more objective options may decrease bias, 71 and provide more accurate estimate of compliance to facemask use in mgs. study designs also may have contributed to variability in results. for instance, two trials, a pilot rct and a non-randomised trial, reported facemask to be significantly effective against respiratory infections at hajj, whereas only two out of six cohort studies reported significant results. in contrast, none of the crosssectional studies yielded significant results. this may indicate that a higher quality study is more likely to produce convincing results. finally, facemask effectiveness also differed depending on the study endpoints. for example, studies that examined effectiveness of facemask against a single respiratory symptom (such as cough, sore throat or fever) either ruled out or did not fully support its effectiveness. 32, 37, 39 this is most likely because singular endpoints are often prone to subjective biases due to their non-specificity. in addition, solitary respiratory symptoms may result from causes other than infections; for instance, cough may result from exposure to dust or smoke during hajj or may be a manifestation of a chronic respiratory condition of non-infectious aetiology, e.g., bronchial asthma. 29 on the other hand, most of the studies that used syndromic criteria (constellation of symptoms) as an endpoint reported facemasks to be effective against respiratory infections during hajj. 18, 20, 22, 26, 28 this is most likely due to the fact that syndromic endpoints are more specific for an illness than a singular symptom. only one study used laboratory-confirmed infection as an endpoint, but its sample size was relatively small (n = 104) and it failed to demonstrate statistically significant protectiveness of facemasks against respiratory viral infections among hajj hcws. 25 similarly, in non-mg settings, effectiveness of facemask varied depending on the study endpoint. [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [72] [73] [74] metaanalysis of rcts involving facemask in non-mgs showed efficacy against ili but not against laboratory-confirmed influenza. 14, 15, 75 this study is the first focussed systematic review that describes both the uptake and effectiveness of facemasks against respiratory infections in mgs, and it compiles a data pool of 12710 participants originating from more than 50 countries. however, the main limitation is that most of the studies were of 'average' or 'below average' quality. there was only one rct but that was a pilot trial of small sample size, and there was another 'trial' published in a nonindexed journal that did not report methodological details including whether and how randomisation was done. as all included studies were conducted only in the context of hajj, it is not possible to generalise the results to other mgs. a large scale clustered rct is currently in its final phase that will measure the efficacy of facemasks against both 'syndromic' and laboratoryconfirmed viral infections. 75 the full results of the trial, once available, are likely to provide firmer evidence on the usefulness of facemask against respiratory infections among attendees of mgs. in summary, the use of facemask among attendees of a particular mg (hajj) remains almost steady with negligible increase throughout the last decade with an average uptake of 50%. facemasks seem to be beneficial against certain respiratory infections during hajj but not definitively proven. professor robert booy has received funding from baxter, csl, gsk, merck, novartis, pfizer, roche, romark and sanofi pasteur for the conduct of sponsored research, travel to present at conferences or consultancy work; all funding received is directed to research accounts at the children's hospital at westmead. dr harunor rashid received fees from pfizer and novartis for consulting or serving on an advisory board. the other authors have declared no 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practical implications for prevention prevalence of preventive behaviors and associated factors during early phase of the h1n1 influenza epidemic widespread public misconception in the early phase of the h1n1 influenza epidemic anticipated and current preventive behaviors in response to an anticipated human-to-human h5n1 epidemic in the hong kong chinese general population factors influencing the wearing of facemasks to prevent the severe acute respiratory syndrome among adult chinese in hong kong hajj pilgrims knowledge about middle east respiratory syndrome coronavirus attitudes and practices concerning middle east respiratory syndrome among umrah and hajj pilgrims in samsun australian hajj pilgrims' knowledge about mers-cov and other respiratory infections public response to the 2009 influenza a h1n1 pandemic: a polling study in five countries influenza seasonality and vaccination timing in tropical and subtropical areas of southern and south-eastern asia air pollution and health -counselling options for physicians validity and reliability of measurement instruments used in research mask use, hand hygiene, and seasonal influenza-like illness among young adults: a randomized intervention trial surgical mask vs n95 respirator for preventing influenza among health care workers: a randomized trial efficacy of face masks and respirators in preventing upper respiratory tract bacterial colonization and co-infection in hospital healthcare workers a clusterrandomised controlled trial to test the efficacy of facemasks in preventing respiratory viral infection among hajj pilgrims the authors would acknowledge the support of ms. trish bennett, manager, medical library, the children's hospital at westmead, nsw, australia, for help with literature search. key: cord-272179-wvw5mmy3 authors: calderaro, adriana; de conto, flora; buttrini, mirko; piccolo, giovanna; montecchini, sara; maccari, clara; martinelli, monica; di maio, alan; ferraglia, francesca; pinardi, federica; montagna, paolo; arcangeletti, maria cristina; chezzi, carlo title: human respiratory viruses, including sars-cov-2, circulating in the winter season 2019-2020 in parma, northern italy date: 2020-10-02 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1473 sha: doc_id: 272179 cord_uid: wvw5mmy3 objectives: this study aimed to determine the prevalence of respiratory virus infections, including sars-cov-2, during december 2019 – march 2020, in a tertiary care hospital-based survey in parma (northern italy). methods: a total of 906 biological samples of respiratory tract were analyzed by both conventional (including culture) and molecular assays targeting sars-cov-2 and the other respiratory viruses nucleic acids. results: 474 samples (52.3%) were positive for at least one virus for a total of 583 viruses detected. single infections were detected in 380 (80.2%) samples and mixed infections were detected in 94 (19.8%). rsv (138/583: 23.7%) and rv (130/583: 22.3%) were the most common viruses identified, followed by sars-cov2 (82/583: 14.1%). rsv predominates until february with 129 detections and drastically decreases in march to 9 detections. sars-cov-2 absent in our area until february 26, in just over a month reached 82 detections. sars-cov-2 was found in mixed infections only in 3 cases all observed in children younger than one year old. conclusions: this study showed a completely different trend between sars-cov-2 and the "common" respiratory viruses that have seen children most affected without distinction of sex, as opposed to sars-cov-2 that have seen adult males the most infected. viral infections of the upper and lower respiratory tracts are among the most common illness in humans, mainly in children and infants in whom the infection can occur 5 to 6 times for year (berry et al, 2015) . briefly, the nucleic acid was extracted from 200 µl of specimens by using the nuclisens® easymag tm extraction assay (biomérieux, france). the nucleic acid amplification was carried out on the applied biosystems 7500 fast dx thermalcycler (applied biosystems, usa) at 25°c for 2 minutes for ung incubation, and then at 50°c for 15 minutes for the reverse transcription step, followed by the enzyme activation step at 95°c for 2 minutes. then, the amplification was carried out for 45 cycles (3 seconds at 95°c and 30 seconds at 55°c). in the prospective analysis, a specimen was considered negative for sars-cov-2 if markers n1 and n3 cycle threshold growth curves do not cross the threshold and the rnase p growth curve cross the line. conversely, if markers cycle threshold growth curve crosses the threshold line, the specimen was considered positive for sars-cov-2 virus. in the retrospective analysis, only n1 marker was used. table 1 ). the distribution of single and mixed infections on the basis of age and sex is shown in figure 1a and 1b, respectively. overall, a total of 583 viruses were detected, rsv (138/583: (table 1) . similarly, the 60.5% (347 out of 574) and the 14.5% (48 out of 332) of the children and adults tested, respectively, were positive (p <0.00001; or: 9.04) for at least one respiratory virus other than sars-cov-2; for this virus the 1.4% (7 out of 513) and the 24% (75 out of 313) of the children and adults tested, respectively, were positive (p <0.00001; or: 0.04) ( table 1) . table 2 (berry et al, 2015) . this suggests that many respiratory pathogens may remain undetected. all novel emergent respiratory viruses have varying but significant impact on human health and the potential to give outbreaks (berry et al, 2015) ; sars-cov-2 as seen in these months, has shown, worldwide, its own unique potential to give epidemics. in this study, we investigated the viral etiology of aris in 906 patients with acute respiratory tract infections, both outpatients and inpatients, attending the tertiary care the samples analysed in this study were sent to the university hospital of parma for routine diagnostic purposes, and the laboratory diagnosis results were reported in the medical records of the patients as answer to a clinical suspicion; ethical approval at the university hospital of parma is required only in cases in which the clinical samples are to be used for applications other than diagnosis. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. identification of new respiratory viruses in the new millennium virological and clinical characterizations of respiratory infections in hospitalized children sars-cov-2 infection diagnosed only by cell culture isolation before the local outbreak in an italian seven-week-old suckling baby matrix-assisted laser desorption/ionization time-of-flight (maldi-tof) mass spectrometry applied to virus identification centers for disease control and prevention. 2020. coronavirus disease genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting wuhan first two months of the 2019 coronavirus disease (covid-19) epidemic in china: real-time surveillance and evaluation with a second derivative model epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in northern italy mammalian diaphanous-related formin-1 restricts early phases of influenza a/nws/33 virus (h1n1) infection in llc-mk2 cells by affecting cytoskeleton dynamics risk factors for sars-cov-2 among patients in the oxford royal college of general practitioners research and surveillance centre primary care network: a cross-sectional study coronaviruses and sars-cov-2 incidence and seasonality of respiratory viruses causing acute respiratory infections in the northern united arab emirates positive rate of rt-pcr detection of sars-cov-2 infection in 4880 cases from one hospital in multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children viruses as sole causative agents of severe acute respiratory tract infections in children mixed respiratory virus infections cresce la popolazione del parmense 2019-ncov (wuhan virus), a novel coronavirus: human-to-human transmission, travel-related cases, and vaccine readiness etiology and clinical outcomes of acute respiratory virus infection in hospitalized adults the outbreak of sars-cov-2 pneumonia calls vaccines respiratory viral infections in infants: causes, clinical symptoms, virology, and immunology respiratory virus surveillance in hospitalised pneumonia patients on the thailand-myanmar border world health organization. 2020. coronavirus disease: situation report -184 epidemiological and molecular surveillance of influenza and respiratory syncytial viruses in children with acute respiratory infections pcr for respiratory viruses other than sars-cov-2 pcr for sars key: cord-259501-iggw1exl authors: kim, yong yean; lew, judy f.; keith, bahareh; telisma, taina; nelson, eric j.; brantly, alexis c.; chavannes, sonese; anilis, gina; yang, yang; liu, mingjin; alam, meer taifur; rashid, mohammed h.; morris, john glenn; madsen beau de rochars, valery e. title: acute respiratory illness in rural haiti date: 2019-02-14 journal: int j infect dis doi: 10.1016/j.ijid.2019.02.003 sha: doc_id: 259501 cord_uid: iggw1exl objectives: acute respiratory infection (ari) is the most common cause of childhood morbidity and mortality in developing countries, including haiti. our objective was to detect pathogens found in children with ari in rural haiti to help develop evidence-based guidelines for treatment and prevention. methods: retrospective study of students with ari at four schools in rural haiti. viral and/or bacterial pathogens were identified by qpcr in 177 nasal swabs collected from april 2013 through november 2015. results: most common viruses detected were rhinovirus (36%), influenza a (16%) and adenovirus (7%), and bacteria were streptococcus pneumoniae (58%) and staphylococcus aureus (28%). compared to older children, children aged 3–5 years had more influenza a (28% vs. 9%, p = 0.002) and adenovirus detected (14% vs. 3%, p = 0.01). similarly, s. pneumoniae was greatest in children 3–5 years old (71% 3–5yrs; 58% 6–15 years; 25% 16–20 years; p = 0.008). children 3–10 years old presented with fever more than children 11–20 years old (22% vs 7%; p = 0.02) and were more often diagnosed with pneumonia (28% vs 4%, p < 0.001). conclusions: younger children had increased fever, pneumonia, and detection of influenza a and s. pneumoniae. these data support the need for influenza and pneumococcus vaccination in early childhood in haiti. hospital-based studies on children in haiti have shown that acute respiratory infection (ari) is the leading cause of child morbidity and mortality (perry et al., 2005; vinekar et al., 2015) . earlier studies in resource-poor settings have identified streptococcus pneumoniae, haemophilus influenzae type b and staphylococcus aureus as important bacterial causes of ari, and respiratory syncytial virus (rsv) and influenza as important viral causes (rudan et al., 2008) . many of these prior studies used technically difficult and labor intensive tests that included bacterial and viral culture (rudan et al., 2008) . the use of diagnostic nucleic acid technology has increased detection of infectious agents associated with ari. a multicountry study that included haiti showed that agents detected in hospitalized children less than 5 years of age who had pneumonia included rsv, influenza a and b, parainfluenza viruses, adenovirus and human metapneumovirus (hmpv) (bénet et al., 2017) . in that same study, analysis of bacterial agents showed high detection of streptococcus pneumoniae and mycoplasma pneumoniae leading the authors to conclude that vaccination efforts for streptococcus pneumoniae will be beneficial. whereas hospital-based studies are informative, most patients do not require hospitalization and much less is known about ari in school-aged children treated at outpatient clinics. in 2012-2013 we assessed outpatient illnesses in children who attended four schools in rural haiti (gressier/leogane) and showed that ari was the most common complaint among 1,357 clinic visits (beau de rochars et al., 2015) . the objective of this retrospective study is to analyze which infectious agents are detected in haitian children presenting with ari in the outpatient setting. knowledge gained from this study will guide clinical care and public health vaccine campaigns. enrollment criteria were all students with complaints of fever and respiratory symptoms who attended one of four schools managed by the christianville foundation network in gressier, haiti. the christianville foundation partners with university of florida (uf) to address public health challenges in the haitian community. these schools were previously described with one having pre-k through 12th grade with approximately 800 students, and three schools having pre-k through the 6th grade with 130-180 students each (beau de rochars et al., 2015) . school clinic staff included one physician and two nurses who evaluated and managed patients as per standard clinic procedures, and obtained a nasal swab from each participant as part of routine clinical care using the bd universal viral transport kit (bd company, franklin lakes, new jersey). given the lack of access to x-ray or pulse oximetry, criteria to obtain swab was based on clinical criteria of history of fever and respiratory symptoms. diagnosis of upper vs lower respiratory infection was based on physical exam. swabs were initially stored at à20 c with testing anticipated soon after collection at the uf laboratory in haiti; due to technical difficulties, de-identified coded swabs were transported in bulk on dry ice to uf and then stored at à80 c until processed. when laboratory studies were completed, clinic staff retrospectively linked a limited clinical data set with results. the study protocol was reviewed and approved by the university of florida irb. samples were thawed on ice and pulse vortexed 5 times. total nucleic acid (including dna and rna) were then isolated using the rtp pathogen kit per manufacturer's protocol (stratec biomedical, birkenfeld, germany). total dna and rna were analyzed by multiplexed rt-pcr using the ftd respiratory pathogen 21 plus kit (fast-track diagnostics, sliema, malta) on an applied biosystems 7500 rt-pcr system. targets were 18 viruses and 5 bacteria: influenza a (flua), influenza b (flub), influenza a/h1n1 (flua/h1n1), rhinovirus (rv), coronaviruses (nl63, 229e, oc43, hku1), parainfluenza (hpiv 1, 2, 3, 4), hmpv a/b (hmpv), bocavirus (bv), mycoplasma table 1 percentage of school children with nasal swabs by school location, age, sex and month/year. * estimated average enrollment during the collection time period. pneumoniae, respiratory syncytial viruses a/b (rsv), adenovirus (hadv), enterovirus (ev), parechovirus (hpev), chlamydia pneumoniae (cp), s. pneumoniae, haemophilus influenzae type b (h. influenzae b), and s. aureus. both ftd respiratory pathogen 21 plus kit controls and independent swab samples known to be positive for rsv, hadv, influenza and coronaviruses were used to validate the results. all patients were examined by the clinical staff. fever was defined as greater than 37.9 degrees celsius. pneumonia was defined as history of fever with cough or congestion and clinical examination findings of crackles, grunting, or decreased breath sounds. two-sided fisher's exact was used to compare the detection rates of agents by age groups, sex, seasonality and clinical parameters, with type i error controlled at 0.05. p-values were not adjusted for multiple comparisons. we also used the fisher's exact test for the co-detection analysis. all tests were conducted using the r software version 3.3. agents detected in 5% of patients were prioritized for analysis. age groups for analytical comparisons were 3-5 years (group a), 6-10 years (group b), 11-15 years (group c) and 16-21 years (group d), with some comparisons using consecutive age groups combined. eight children had samples obtained twice and their visits were separated by an average of 6 months (2-17 months). given the passage of at least 2 months, each patient encounter (i.e., sample) was considered a unique entity for analysis. swabs were collected from 177 children attending four different schools during school attendance from april 2013 through november 2015: school a (75%), school b (17%), school c (6%) and school d (2%). the average age was 8.7 years (range = 3-20 years); female sex = 54%. a total of 76% of samples (133/174) with date information were collected during the september to june school year of 2013-14, two samples were collected in april 2013 (1%), and the remainder 22% (39) were collected from february-june (excluding december-january) and august-november of 2015 [ table 1 ]. given that etiology of ari changes by age, we first looked at agents detected by age. younger children had flua, hadv and s. pneumoniae detected more often than older children, while s. aureus detection peaked in children with ages between the youngest and oldest age groups. analysis of viruses showed that more children in age group a had flua detected (28%) when compared to groups b (10.5%, p = 0.02), c (4%, p = 0.01), and d (11%, p = 0.10). significantly more children in age group a had hadv (14%) detected than children in groups b-d combined (3%), p = 0.01. for bacterial agents, s. pneumoniae detection was greatest in children in the age group a (71%) followed by groups b (58%) and c (59%), with the least in d (25%). significantly more group a-c children had s. pneumoniae detected (64%) than those in group d (25%), p < 0.001. although h. influenzae b detection decreased with age, this difference was not statistically significant. for s. aureus, table 2 viruses and bacteria detected in children by age. p value obtained using two-sided fisher's exact. detection was highest in the group b-c children (43%), with significantly less s. aureus detected in groups a (14%) and d (14%), both p < 0.01 [ table 2 ]. the mean number of total agents detected per child in age groups a, b and c was higher at 1.9-2.0 than in group d at 1.2. significantly more children in age groups a (62%), b (58%) and c (74%) had 2 or more agents detected than children in group d (32%), p < 0.04 for each comparison to group d. analysis of the number of viral agents detected showed no significant difference was seen between the proportion of children who had !1 viral agents detected between age groups a (77%), b (67%), c (67%) or d (68%). however, significantly more bacterial agents were detected in age groups a, b and c children than in group d. the proportion of children with !1 bacterial agent(s) detected per age group were: groups a (75%), b (82%), and c (81%) versus group d (36%), p < 0.001 for each comparison to group d. the most common viruses detected in children overall with fever and respiratory complaints (n = 177) were rv (36%), flua (16%, including 13% due to flua/h1n1) and hadv (7%). more rarely detected were rsv, bv and hpev. s. pneumoniae was the most common bacteria detected at 58%, followed by s. aureus at 28%, and h. influenzae b at 3%. [supplemental table s1 ] co-detection was common with 322 agents detected in 177 patient samples. at least one viral agent (range 1-3) was detected in 71% of children and at least one bacterial agent in 72% (range 1-3), with 18% having greater than 1 virus and 18% with greater than 1 bacterial spp. detected in the 177 patient samples. only 10 children (5.6%) had no agent detected. the average number of any agent detected (viruses + bacteria) per child was 1.8 [ table 3 ]. analysis by age groups showed no significant difference in viral detection. however, when looking at bacterial detection and co-detection of two or more agents, the oldest age group d had significantly less frequent detection (p < 0.001 for bacteria, p = 0.031 for co-detection of two or more agents). more children had flua as the sole pathogen (39%) than those who solely had hadv (0%, p = 0.017), ev (0%, p = 0.017), or s. pneumoniae (19%, p = 0.04) detected. co-viral detection was less common in children with flua (21%) than in children with hadv (83%, p < 0.001) and ev (100%, p < 0.001). co-bacterial detection was also less common in children with flua (57%) than in children with hadv (100%, p = 0.007) and ev (91%, p = 0.063) [ table 4 ]. evaluation for relationships between specific agents showed that ev was 100% correlated with concurrent rv detection (11/11, p < 0.001); both picornaviruses having possible correlates by pcr. in contrast, flua and flub was negatively correlated with rv detection (p = 0.0022 and p = 0.027, respectively). evaluation between viral and bacterial correlates showed 100% of children with hadv also had s. pneumoniae detected (12/12, p = 0.0014). detection of s. aureus was negatively associated with that of flua; despite 27.7% of all children having s. aureus detected, none of the 28 children with flua detected were co-detected with s. aureus, p < 0.001. no other agents showed significant co-detection relationship. no significant differences were found between females and males regarding total viral plus bacterial agents, total viral or bacterial agents, or specific agents detected by pcr. table 3 co-detection in children with ari by age. of 174 samples that had date of collection data, 133 (76%) were collected from children during the school year of september 2013 through june 2014 for this one season evaluation. the number of children tested were not evenly distributed with 1-6 tested in sep, oct, dec, feb, mar, jun and 13-57 tested in nov, jan, apr, may. analysis of specific agents detected monthly showed seasonality was significantly associated with influenza detection. more children had flua/h1n1 detected during the months of oct-dec 2013 (14/63, 22%) than children during the school year outside of those months (0/70, 0%, p < 0.001) [ figure 1 ]. similarly, more children had any flu (a/h1n1 + a/not h1n1 + b) detected in oct-dec 2013 (16/63, 25%) compared with those in the other 2013-14 school months combined (8/70, 11%, p = 0.044). although no other agents with at least a 5% (7 of 134) detection rate were found to table 4 co-detection of agents from 179 children with respiratory complaints in an out-patient setting. have seasonality, it was noted that all rsv detected occurred in nov 2013 and rsv detection was more common in nov 2013 (4/57, 7%) than in the other school year months combined (0/76, 0%, p = 0.032). of 158 children who had clinical data, primary diagnoses were upper respiratory tract infection (urti, excludes group a streptococcal [gas] pharyngitis) at 67%, lower respiratory tract infection (lrti) at 21% and 'other' at 12%. twenty-five (16%) children had more than 1 diagnosis. fever was detected at the time of presentation in 28 (18%) children and was significantly more common in children with lrti (24%) or with 'other' diagnoses (53%) when compared to those with urti (9%), p 0.04 for both analyses [ table 5 ]. fever and specific virus analysis showed a significantly higher percentage of children detected with flua (50%), separately flua/ h1n1 (47%), and flua or flub (48%) had fever recorded compared to those with rv (12%). for bacteria detection, neither s. pneumoniae or s. aureus were associated with fever when compared to children without s. pneumoniae or s. aureus, respectively. analysis of specific viral or bacterial agents detected showed more children with flua or flub had lrti (33%) compared to urti (15%) [ table 5 ]. none of the 6 children with primary diagnosis of tonsillitis had any viruses detected, whereas 5/8 (63%) with primary diagnoses of parasitosis or febrile syndrome had flua/h1n1 or hadv detected. [data not shown] fever and lrti separately were associated with the younger age groups. significantly more children aged 3-10 years had fever detected (22%) when compared to children aged 11-20 years (7%, p = 0.02). similarly, lrti was more common in 3-5 year old children (36%) compared to those 6-10 years (19%), 11-15 years (8%), and 16-20 years (0/21, 0%), and this was statistically significant when comparing groups a-b (28%) to c-d (4%), p < 0.001. evaluation of medications given showed only 2 of 158 (1.3%) children did not receive any medications. antibiotics were given to 44 (27.7%) children that included 31 (94%) diagnosed with lrti with the rest attributed to primary-or co-diagnoses of tonsillitis, bacterial skin, urinary tract or sinus infections. of the 31 with lrti, 30 received amoxicillin and 1 co-trimoxazole. overall, the three most common medications given were acetaminophen (74%, 117), mucolytic +/à beta agonist +/à expectorant mix (52%, 83), and vitamin c (47%, 74). for the 101 children with uncomplicated uri diagnosis (no concurrent known bacterial infections), 22% received one, 69% two, and 7% all three of these drugs. compared to children diagnosed with uncomplicated uri, children with lrtis or 'other' diagnoses did not significantly differ in percent receiving these medications. this is one of the largest retrospective studies of pediatric outpatients with ari in rural haiti. the overall findings of rv as the most common virus detected followed by influenza in haiti is comparable to that found in studies of children in other tropical, resource-poor countries (hoffman et al., 2012; schlaudecker et al., 2012; taylor et al., 2017) . however, hmpv in children with ari was detected less often (3%) in this study compared to similar studies (11-14%) (al-sonboli et al., 2006; banerjee et al., 2007; taylor et al., 2017) . these and other studies showed hmpv caused a high percentage of severe ari in those <2-5 years of age (ali et al., 2013; panda et al., 2014) , suggesting the lower detection rate seen in this study may be due to the older median age in this study, and differences between outpatient study compared to previous inpatient studies. rsv detection was significantly lower at only 2.3% of tested patients compared to previously published reports of 30-40% in other developing countries where the bulk of the children were seen in hospitals or emergency rooms (mccracken et al., 2013; dawood et al., 2015; bouzas et al., 2016) . this low level of detection may have been due to initial storage of nasal swabs at à20 c which has been found to decrease rsv detection (nunes and moura, 2006) and our patients being 3-20 years old when the highest rate of the rsv positivity are typically among children 2 years of age. low detection of rsv was also seen in a study of 4,242 pediatric patients that showed detection of rsv infection at 3.4 à7.2% in older children 3-14 years of age compared to 18.7-29.2% in 4 months to 2 years old (liu et al., 2014) . it is possible that by the time haitian children are 3 years of age, the risk for significant infection has greatly declined in comparison to those in less resource poor countries where rsv and hmpv can continue to cause significant disease in those <5 years old. future studies on rsv and hmpv that included children <3 years of age in both outand in-patient setting could help better understand their clinical impact. consistent with other studies is the finding that detection of influenza (a, including a/h1n1, and b) was significantly associated with increased clinical symptoms of fever at presentation and lrti diagnosis especially in younger children (laforce et al., 1994; cox and subbarao, 2000; descalzo et al., 2016) . introduction of flua and flub vaccine in younger and school aged children could significantly decrease its clinical impact, including decrease spread to siblings and adults at home. a study that ascertained peak influenza activity in 70 tropical or subtropical countries suggested that timing of influenza vaccine in haiti should be in april based on data from nearby countries including cuba and dominican republic (no haiti data) (hirve et al., 2016 ). yet in this evaluation of children in haiti for the school year of 2013-14, the peak detection of influenza appeared to be in oct-dec 2013. this finding suggests that immunization in haiti should begin by august/september, similar to october for mexico, guatemala and jamaica in the 70 nation study. increased testing in haiti for peak detection over several years is needed to determine best timing of influenza vaccinations. the high detection rate of s. pneumoniae (58%) and h. influenzae b (3.4%) compared to affluent countries may reflect the lack of s. pneumoniae vaccine in the immunization program in haiti and limited h. influenzae b vaccinations which only began in late 2012 (mbelle et al., 1999; abdullahi et al., 2008; agrawal and murphy, 2011; who, 2013a; adegbola et al., 2014) . agent-specific vaccination has been shown to decrease s. pneumoniae and h. influenzae b colonization and subsequent infection in children (dagan et al., 2002; agrawal and murphy, 2011; alvarez et al., 2016) . the decrease in s. pneumoniae and h. influenzae b detection with increased age is likely attributed to protective antibodies developing due to infections (mbelle et al. 1999; dagan et al., 2002; peraza et al., 2004) . despite this decrease, the high colonization rates and associated risk for infection strongly supports introduction of s. pneumoniae and continuation of h. influenzae b vaccine in those <5 years of age (who, 2013b; who, 2012) . furthermore, future determination of the s. pneumoniae serotypes found in 58% of the overall cohort could help identify the usefulness of available vaccines. although multiple studies of lrti in developing countries have implicated infection with s. pneumoniae, h. influenza type b and s. aureus as the major bacterial causes of severe pneumonia (shann, 1995) , this study detected high rates of these pathogens in nonsevere outpatients. possibly the problem of high rates of colonization could have masked some primary or secondary bacterial infections. future studies may benefit from blood cultures along with pcr to assess disease burden and from more extensive patient follow-up. in addition, community case-control studies and studies where the incidence of pneumonia is measured pre-and postvaccination may clarify disease burden and attributable fraction of colonization versus active disease from these pathogens (rudan et al., 2008; levine et al., 2012; morpeth et al., 2017) . the 20% incidence of lrti in this ari study is consistent with previous findings that 10-20% of children with ari may develop pneumonia (panda et al., 2014) . virtually all patients who had lrti diagnosed were treated with an antibiotic considered appropriate by the world health organization (who, 2014). however, >50% of patients received one or more "common cold" medications that are generally not advised by who, particularly in young children (who, 2001) . the risks/benefits of such medications are an issue in both resource rich and poor countries, but the latter have an additional fiscal burden related to treatments that may have unproven efficacy and potential toxicities. limitations of the study are related to the developing world setting. as discussed above, due to the use of nasal swabs with pcr based detection, we can comment on the pathogens detected at the time of symptoms but cannot directly point to the pathogen as the etiology. the lack of corresponding tests for the diagnosis of pneumonia such as chest x-ray, pulse oximetry, or blood culture is due to lack of resources in the rural clinic setting. another resource related issue is the skewing of the patient population to the younger age group since only one out of the four schools provides middle school or high school education. also there are gaps in data during the vacations and holidays when schools are closed such as for winter vacation in december which may present a bias in the data. lastly, since the school clinic was in location a, children who were ill in other locations enrolled on the study were less able to travel to the clinic which likely presented a bias based on resource distribution. in conclusion, school-aged children in rural haiti between 3 and 5 years old had influenza a and streptococcus pneumoniae detected and pneumonia diagnosed more often than older children. the children presenting with these agents detected in this outpatient study were less ill compared to previous inpatient studies. future research should include community-based case-control studies to assess colonization versus active infection. this study also supports ongoing advocacy for influenza and pneumococcal vaccines in young haitian children. pre-post studies (e.g. a stepped wedge design) during these vaccination campaigns would define the impact of vaccination and further characterize the morbidity and mortality associated with the pathogens detected herein. this work was supported by the university of florida foundation, inc. through the emerging pathogens institute at university of florida; and the university of florida department of pediatrics, pediatrics medical education. the descriptive epidemiology of streptococcus pneumoniae and haemophilus influenzae nasopharyngeal carriage in children and adults in kilifi district carriage of streptococcus pneumoniae and other respiratory bacterial pathogens in low and lower-middle income countries: a systematic review and meta-analysis haemophilus influenae infections in the h. influenzae type b conjugate vaccine era human metapneumovirus and respiratory syncytial virus in children role of human metapneumonvirus, influenza a virus and resipiratory syncytial virus in causing who-defined severe pneumonia in children in a developing country potential reduction of mortality from invasive pneumococcal infection among children with sickle cell disease in haiti human metapneumovirus infections amoung children with acute respiratory infections seen in a large referral hospital in india spectrum of outpatient illness in a school-based cohort in haiti, with a focus on diarrheal pathogens microorganisms associated with pneumonia in children <5 years of age in developing and emerging countries: the gabriel pneumonia multicenter, prospective, casecontrol study respiratory syncytial virus a and b display different temporal patterns in a 4-year prospective cross-sectional study among children with acute respiratory infection in a tropical city global epidemiology of influenza: past and present reduction of nasopharyngeal carriage of streptococcus pneumoniae after administration of a 9-valent pneumococcal conjugate vaccine to toddlers attending day care centers what is the added benefit of oropharyngeal swabs compared to nasal swabs alone for respiratory virus detection in hospitalized children aged <10 years estimating the burden of influenza-associated hospitalizations and deaths in central america influenza seasonality in the tropics and subtropics -when to vaccinate? viral and atypical bacterial etiology of acute respiratory infections in children under 5 years old living in a rural tropical area of madagascar influenza: virology, epidemiology, disease, and prevention the pneumonia etiologu research for child health project: a 21st century childhood pneumonia etiology study epidemiology of acute respiratory infections in children in guangzhou: a three-year study immunogenicity and impact on nasopharyngeal carriage of a nonavalent pneumococcal conjugate vaccine respiratory syncytial virus infection in guatemala detection of pneumococcocal dna in blood by polymerase chain reaction for diagnosing pneumococcal pneumonia in young children form low and niddleincome countries isolation of respiratory syncytial virus from nasopharyngeal aspirates stored at 20 degrees c from one to fifteen months after collection naturally acquired immunity to haemophilus influenzae type b in healthy cuban children assessing the causes of under-five mortality in the albert schweitzer hospital service area of rural haiti epidemiology and etiology of childhood pneumonia etiology and seasonality of viral respiratory infections in rural honduran children the management of pneumonia in children in developing countries respiratory viruses and influenza-like illness: epidemiology and outcomes in children aged 6 months to 10 years in a multi-country population sample hospitalizations and deaths because of respiratory and diarrheal diseases among haitian children under five years of age world health organization. cough and cold remedies for the treatment of acute respiratory infections in young children world health organization. pneumococcal vaccine who position paper -2012 new vaccine protects haitian children from five diseases haemophilus influenzae type b (hib) vaccination position paper world health organization. revised who classification and treatment of childhood pneumonia at health facilities: evidence summaries we thank the children and their parents for their willingness to participate in this study as well as the tireless contributions of the christianville foundation to collaborate in this impactful study. respiratory swab samples known to be positive for rsv, adenovirus, influenza and coronaviruses were generously donated by dr. kenneth rand and howard rampersaud at the university of florida shands hospital. none. we have read and complied with the policy of the journal on ethical consent as stated in the guide to authors. this study was reviewed and approved by the university of florida irb. supplementary data associated with this article can be found, in the online version, at https://doi.org/10.1016/j.ijid.2019.02.003. key: cord-261058-yu2qw02l authors: burgner, david; harnden, anthony title: kawasaki disease: what is the epidemiology telling us about the etiology? date: 2005-06-03 journal: int j infect dis doi: 10.1016/j.ijid.2005.03.002 sha: doc_id: 261058 cord_uid: yu2qw02l kawasaki disease (kd) is an important and common inflammatory vasculitis of early childhood with a striking predilection for the coronary arteries. it is the predominant cause of paediatric acquired heart disease in developed countries. despite 40 years of research, the aetiology of kd remains unknown and consequently there is no diagnostic test and treatment is non-specific and sub-optimal. the consensus is that kd is due to one or more widely distributed infectious agent(s), which evoke an abnormal immunological response in genetically susceptible individuals. the epidemiology of kd has been extensively investigated in many populations and provides much of the supporting evidence for the consensus regarding etiology. these epidemiological data are reviewed here, in the context of the etiopathogenesis. it is suggested that these data provide additional clues regarding the cause of kd and may account for some of the continuing controversies in the field. kawasaki disease; vasculitis; genetics; epidemiology; inflammation summary kawasaki disease (kd) is an important and common inflammatory vasculitis of early childhood with a striking predilection for the coronary arteries. it is the predominant cause of paediatric acquired heart disease in developed countries. despite 40 years of research, the aetiology of kd remains unknown and consequently there is no diagnostic test and treatment is non-specific and sub-optimal. the consensus is that kd is due to one or more widely distributed infectious agent(s), which evoke an abnormal immunological response in genetically susceptible individuals. the epidemiology of kd has been extensively investigated in many populations and provides much of the supporting evidence for the consensus regarding etiology. these epidemiological data are reviewed here, in the context of the etiopathogenesis. it is suggested that these data provide additional clues regarding the cause of kd and may account for some of the continuing controversies in the field. # 2005 international society for infectious diseases. published by elsevier ltd. all rights reserved. no predefined order and some may even be absent on presentation. in many children the clinical presentation is striking and kd patients are often misdiagnosed with severe sepsis. however, kd can have similar clinical features to other common childhood illnesses, such as measles, rubella and scarlet fever. these children may present a diagnostic challenge 6 and the lack of a specific diagnostic test may delay treatment and thus worsen prognosis. 7 moreover, to confuse the clinical picture further, there is increasing concern that the diagnostic criteria are too narrow. 'atypical' or 'incomplete' kd is a description used for children presenting with the characteristic fever but fewer than four classical signs. a better descriptive term is 'incomplete kd' because these children do not demonstrate atypical signs, just fewer of them. cervical lymphadenopathy is the least commonly observed of the diagnostic criteria, occurring in about three quarters of usually older children, whilst prolonged fever and peripheral desquamation have been reported as the commonest diagnostic features. incomplete kd may be poorly recognised and occurs more often in infants. 8 children presenting with incomplete kd are at higher risk of developing coronary artery lesions both because of their young age and their potential for not receiving timely immunoglobulin treatment. 8 interestingly, as many as 10% of the children reported in the original report of the syndrome 2 would not fulfil the current case definition. 3 the clinical diagnostic criteria need refinement to increase their positive predictive value and recent guidelines have been developed in an attempt to increase the sensitivity of the clinical diagnosis. 5 it is unclear how these will perform in clinical practice. although these guidelines are intended only as a clinical tool, they are likely to have an impact on the reported epidemiology of kd. kawasaki disease is clearly not the benign childhood exanthem initially proposed 1,2 and has significant long-term implications. kawasaki disease is the most common cause of paediatric acquired heart disease in the world. 3 coronary artery lesions (predominantly aneurysms) occur in up to 30% of untreated and 5-10% of treated children; 1, 9, 10 the poor outcome despite adequate treatment reflects an incomplete understanding of the etiopathogenesis. acute mortality in kd is increased significantly, with deaths predominantly occurring from myocardial infarction following occlusion of giant coronary aneurysms. 11, 12 overall, myocardial infarction occurs in 2% of those with coronary artery lesions. 13 lifelong medical therapy, coronary artery grafting and even heart transplantation may be required. 1 crucially, in children without coronary artery lesions who die of other causes, the coronary arteries are almost invariably markedly abnormal, with striking pro-atherosclerotic changes. 14, 15 abnormal in vivo function in non-coronary arteries 16 suggests that cardiovascular damage post-kd is both pervasive and persistent, even in the absence of acute coronary artery lesions. thus, there is intense speculation that kd is pro-atherosclerotic, but definitive long-term data are lacking. regressed coronary artery lesions result in abnormal coronary artery function 17 and histological changes that are pro-atherosclerotic. 15, 18 the similarities between kd and adult cardiovascular pathology suggest that kd may be a useful paradigm for investigating the etiopathogenesis of atherosclerosis. 19 does kawasaki disease represent an extreme phenotype of a more pervasive phenomenon? it is possible that kd is not a distinct entity, but the more clinically obvious end of a spectrum of pathogenic processes. kd may therefore reflect an extreme clinical phenotype where childhood infections predispose to subsequent endothelial damage and cardiovascular pathology. thus in genetically susceptible children, acute infections such as those causing fever and rash, may result in unrecognised damage to the cardiovascular system that later manifests itself as adult cardiovascular disease. adult atherosclerotic disease (like kd) has not been reliably associated with a single infectious etiology, but correlates with overall infectious burden. 20 furthermore, acute childhood infections are accompanied by pro-atherosclerotic phenomena and subsequent thickening of the arterial intima. 21 understanding the etiopathogenesis of kd may therefore identify common gene-environment interactions that are involved in adult cardiovascular disease. why is it important to understand the etiology and pathogenesis of kawasaki disease? the timely diagnosis of kd is essential in maximising the prevention of overt coronary damage; treatment beyond ten days of onset is associated with a worse outcome and an increased incidence of coronary abnormalities. 22, 23 the lack of a specific diagnostic test and the limited clinical utility of the current clinical diagnostic criteria mean that the diagnosis is often delayed, even in populations where the condition is well recognised. 24 the currently accepted best treatment (intravenous immunoglobulin and aspirin (table 2) 6 fails to prevent coronary artery abnormalities (identifiable by imaging) in up to 10% of cases. 25 specific diagnostic test(s) and rational interventions could be readily developed if the etiopathogenesis of kd was fully understood. moreover, preventative treatments such as vaccines would be justified in populations with the highest kd incidence, where kd affects 1-2% of all children, such as korea and japan. 3 the consensus view is that kd results from a widely distributed infectious agent (or possibly agents) that causes the clinical syndrome in genetically susceptible children. much of the supporting data for this viewpoint is provided by epidemiological studies in a variety of populations. kd is described in all ethnic groups, but the incidence varies dramatically (see below). the homogeneity of the clinical phenotype and epidemiology suggest that kd arises from common disease processes, although the antigenic trigger(s) and/or the genetic determinants may differ between populations. kawasaki disease shows a striking age distribution reminiscent of other childhood infections. over 80% of cases occur between the ages of six months and four years, 26 although the condition occurs rarely both earlier 27 and later 28 in life. the low incidence of kd in both the first six months suggests that most infants are protected by passively acquired maternal antibody against the causative agent(s). a transient immunological immaturity may also account for the low incidence in the first few months postnatally. 29 the low incidence of kd beyond mid-childhood suggest a ubiquitous antigen(s) that most children encounter uneventfully in early childhood and to which they mount an appropriate and protective immune response. kawasaki disease is more common in boys (male:female ratio 1.6:1) 1 a feature observed in many infectious diseases 30, 31 and also in coronary atherosclerosis, where sex differences in immune responses are suggested to mediate susceptibility. 32 seasonal variation in kd incidence is well recognised, but the predominant season varies in different countries. in the uk, 33 australia 24 and the usa 34,35 kd is most common in winter and spring. in china, spring and summer predominate 36 and in korea kd incidence is highest in summer months. 37 in japan, which reports the highest kd incidence, table 2 treatment of kawasaki disease (for detailed discussion of the treatment of kawasaki disease see references 5,6,97 ). at a dose of 2 g/kg given as a single infusion over 10-12 hours (unless cardiac status necessitates infusing the dose more slowly or in divided doses). failure to respond to this initial ivig dose is usually treated with a second dose (usually 2 g/kg as a single infusion). failure to respond to the second ivig dose is often treated with intravenous methylprednisolone under expert supervision the dose of aspirin is controversial and its utility has never been proven in a randomised controlled trial. it remains, however, part of the standard management of kd. generally 'high dose' aspirin (50-100 mg/kg/day in divided doses) is given acutely until the fever defervesces, when 'low dose' aspirin (2-5 mg/kg/day) is given until an echocardiogram at six weeks after the kd diagnosis is normal. if the six week echocardiogram is abnormal, aspirin is usually continued under cardiological supervision anti-cytokine therapies and other interventions are generally unproven but have occasionally been used. for a review see newburger and fullton 5 the seasonal variation is less marked. 38 one possible explanation for these divergent data is that season is a marker for weather conditions that have a more direct role in determining the incidence. in the us, kd incidence clearly correlates negatively with average ambient temperature and positively with average rainfall in the preceding month. 39 studies are underway investigating similar parameters in the uk. it is unknown whether the meteorological conditions themselves predispose to kd, or, more plausibly, if they alter the epidemiology of etiological agents. the lack of consistent seasonal associations in different countries raises the possibility that various etiological agents may be involved in the etiology of kd. geographical clustering of kd cases and epidemics have been reported from a number of countries, 40-44 although they have been much less frequently reported in the past decade, possibly suggesting a changing epidemiology. in japan, which has provided the most comprehensive epidemiological data, epidemics of kd have been described with a clear epicentre and documented geographical spread across the whole nation within six months. 42 these epidemiological data clearly indicate an infectious etiology for kd. the clinical features of the disease are also characteristic of a severe acute childhood infection. it seems likely that the causative agents are widely distributed and are also highly immunogenic, at least in most children, as more than one episode of kd is rare. recurrent kd is reported in 1-3% of children, 45 although it appears less common in caucasians. 46 it may reflect a specific immunological deficiency in these children or exposure to more than one causative agent. 3 various environmental causes of kd have been repeatedly suggested (table 3) , but none has been consistently replicated. however, the possibility of environmental factors influencing etiology, possibly by modulating infection risk, remains a possibility. the search for a single unifying microbiological cause has been unrelenting but, to date, fruitless. standard microbiological techniques, molecular methods and serological investigations have so far failed to identify an etiological agent. molecular techniques fail to detect circulating conserved microbial sequences in kd, 47 indicating that the antigenic stimulus may arise from a distant site (e.g. colonising pathogens in the nasopharynx) and/or may represent host-derived factor(s) that induce or promote the pro-inflammatory cascade. the list of discarded and/or unproven etiological agents in kd is long (table 3) . a recent report of an association between the presence of genetic material from a novel coronavirus and kawasaki disease in a handful of cases 48 remains unproven and may reflect an epiphenomenon; the putative etiological agent is a relatively common viral pathogen in young children and it is unclear how long the dna persists. the lack of a unifying etiological agent despite a significant research effort suggests that kd can follow exposure to more than one infectious agent, or that a novel infectious agent is involved. alternatively the clinical phenotype may reflect a stereotyped response in a genetically-susceptible host to one of a variety of infectious agents. much of the continuing debate in the literature concerns whether kd is caused by a superantigen 49 or a conventional antigen. 50 kd shares many clinical features with superantigen-mediated diseases (for example, rash, conjunctivitis and skin peeling) and kd has occasionally been reported concurrently in children with toxic-shock syndrome, which is caused by superantigens. 51 however, unequivocal epidemiological and laboratory support for a role for superantigens in kd is lacking. in one small study, maternal antibodies against toxic shock syndrome toxin-1 appeared protective against early-onset kd. 52 however, the carriage rates of superantigen-producing bacteria by children with kd are not consistently increased, 53, 54 although these data may reflect the involvement of as yet unidentified 188 d. burgner, a. harnden superantigens, with more than one superantigen capable of causing kd. superantigens bind to the vb region of the t-cell receptor and clonal expansion of vb2-expressing t-cells has been reported in some studies of kd, 55 but again the finding is inconsistent. 56 other studies have reported oligoclonal igaproducing plasma cells infiltrating bronchial and intestinal tissues in fatal kd, 57 which suggests the involvement of a conventional antigen. much of the controversy and inconsistency surrounding the nature of the infectious trigger in kd might reflect multiple etiological agents resulting in the same clinical phenotype. it is possible, for example, that a viral upper respiratory tract infection may alter local immunity and allow elaboration of superantigens by colonising bacteria in the nasopharynx. certainly the epidemiology of kd, with rapid changes in incidence, seasonal variation and the relationship between incidence and weather conditions is more redolent of acute viral infections 58,59 than bacterial colonisation, which alters more slowly. 60 in meningococcal disease, influenza infection acts in an analogous way, and meningococcal epidemics often follow influenza outbreaks. 61, 62 this hypothesis could be addressed through large detailed prospective epidemiological studies. another possibility is that either pathogen or host factors modulate the behaviour of an antigen, so that it behaves both as a conventional antigen and as a superantigen. heat shock proteins are increased in acute inflammatory conditions, including kd 63 and cross-reactivity with certain heat shock proteins is thought to be responsible for the inflammation of the bcg scar in kd. 64 heat shock proteins have been reported to alter the behaviour of superantigens, so that the immune system recognises them as conventional antigens 65 and also can greatly up-regulate pro-inflammatory responses to conventional antigens. 66 the possibility of endogenous stimuli that profoundly suppress or enhance antigenic effects has not previously been considered in kd, but might account for much of the controversy surrounding the roles of conventional or superantigens. whatever the etiological trigger(s) for kd, there is clear evidence that host genetic determinants play a major role in both susceptibility and probably outcome in kd. genetic studies of kd are therefore likely to be highly informative about etiology and pathogenesis. although kd is reported in all ethnic groups, the variation in incidence of kd between (and to a lesser extent within) countries is striking. the annual incidence varies from approximately three (per 100,000 children <5 years of age) in south america, to four in australia, 24 eight in the uk, 33 4-15 in the us, 1 20-30 in china 36 and hong kong 67 50 in taiwan, 68 90 in korea 37 and >130 in japan 69 the reported incidence is probably underestimated in many countries as atypical cases are not included. australian data (burgner et al., unpublished) suggest an incidence 50% higher than that recorded through active surveillance. 24 in a number of countries the incidence of kd appears to be increasing. 33, 68, 69 whilst this may be partly attributable to increased awareness, the increasing incidence is reported in countries where the disease has been widely recognised for several years and where a standard case definition is employed and may therefore reflect changing epidemiology. the incidence of kd is therefore greatest in north-east asians, especially in koreans and japanese. it is estimated that 1-2% of all hospitalised korean children have kd (park yw, personal communication) and that kd affects one in 150 japanese children. 3 this indicates genetic factors may be central in determining susceptibility, especially as the incidence rate remains high in those migrating to lower incidence countries. for example, the incidence of kd in japanese americans in hawaii (135/100,000 <5 years) is identical to the highest rates reported from japanese living in japan. 67 the incidence rate in siblings of affected children is 10-15 fold higher than the population incidence in japan. 70 the ratio of sibling to population incidence is termed the 'heritability' or 'l s '. sibling rates outside japan are unknown, but reports from caucasians support this trend 71 and sibling rates in korea 37 (burgner, unpublished observations) also support this high heritability. this figure is slightly less than the heritability for insulin-dependent diabetes (l s 15) and 4 times higher than that of asthma, 72 suggesting a striking genetic predisposition to develop the disease in a minority of children across different ethnic groups. in addition, the incidence of previous kd in parents of japanese children with kd is significantly increased and these families are much more likely to have other affected children and children with recurrent disease. 73 taken together, these epidemiological data provide convincing evidence for a major role for host genetics in kd susceptibility. whilst there are concerns that cardiovascular damage may be pervasive in kd, overt coronary artery lesions only develop in a minority of children. in acute kd all arms of the innate and adaptive immune response are activated, but lymphocytes, macrophages and neutrophils are central. 74 the extent and kinetics of host inflammation strongly correlates with the risk of coronary damage. the duration of fever prior to treatment, 75-77 the maximal erythrocyte sedimentation rate, 78 the extent of pro-inflammatory cytokine production 79, 80 and the degree of neutrophil activation 81 have all been shown to be risk factors for coronary damage. the extent of the host inflammatory response is partly genetically determined. 82 genetic factors are therefore likely to be important in determining outcome in kd and genetic studies may identify key pathogenic mediators and ultimately guide the development of new interventions. kawasaki disease is likely to be a genetically 'complex disease', with contributions from a number of genetic loci to susceptibility and outcome. associations between genetic variants at candidate loci and kd susceptibility and outcome may be extremely informative about the role of specific mediators in etiopathogenesis, allowing investigation of hypotheses suggested by the clinical data, but untestable by conventional clinical or laboratory studies. the consensus view supports the concept of a genetically-susceptible host in kd 6, 83 and there is growing realisation that immunogenetic studies may reveal much about the disease and improve diagnosis, treatment and prognosis. immunogenetic data suggest a number of plausible associations. many studies focus on putative downstream outcome determinants and suggest a role for mediators of innate inflammation, 84 endothelial activation 85 and cardiovascular homeostasis. 86 studies of susceptibility determinants are more limited. there are associations with class i regions of the human leucocyte antigen (hla) in japanese, 87 with different alleles associated in caucasians. 88 however, these hla studies are largely historical and further work using modern hla typing techniques are warranted. unfortunately, genetic studies of kd have often been undermined by methodological problems 89 that dog many such studies of human complex disease. thus some of the reported associations are likely to be false positive results. in particular, the studies often lack statistical power, employ multiple uncorrected statistical comparisons and many do not replicate findings in an independent population. 87, 88, [90] [91] [92] case-control methodology in a multi-ethnic disease may yield spurious disease associations (type i errors) due to population admixture, 93 unless this is actively identified. 94 inadequate marker density in candidate loci, where the functional variants are unknown, may increase type ii errors. 89 kawasaki disease is a fascinating and important paediatric illness, which presents a significant diagnostic challenge. it is the most common cause of heart disease acquired in childhood and an important paradigm for understanding the determinants of adult cardiovascular pathology. the epidemiology is well characterised and clearly supports the view that the disease results from an inappropriate immunological response to one or more infectious triggers in genetically-susceptible individuals. the search for the microbial etiology has been disappointing and unsuccessful and all that remains of over three decades of such studies is a 'long list of discarded pathogens'. 3 understanding the genetic determinants of susceptibility to kd and those involved in mediating coronary artery damage may be a more profitable approach. the methodological issues that have undermined genetic analyses can be largely overcome by international collaborative studies that employ standardised phenotypic definitions and large sample sizes derived from different ethnic groups. the use of familybased genetic association analyses 95 circumvents the problems of population stratification and the use of trans-racial mapping (i.e. investigating genetic determinants in different ethnic groups) 96 may prove important to defining the critical genetic determinants, particularly in regions of high linkage disequilibrium. newer molecular techniques, particularly gene expression profiling and proteomics may identify novel molecular 'fingerprints' that differentiate kd from other febrile and inflammatory illnesses. 3 the mystery of kd may ultimately be solved by looking within the host. kawasaki disease: a brief history acute febrile mucocutaneous syndrome with lymphoid involvement with specific desquamation of 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complex outcomes the hla class ii region and susceptibility to kawasaki disease polymorphism of transmembrane region of mica gene and kawasaki disease polymorphism of slc11a1 (formerly nramp1) gene confers susceptibility to kawasaki disease mapping disease genes: family-based association studies control of confounding of genetic associations in stratified populations the tdt and other family-based tests for linkage disequilibrium and association identification of susceptibility loci for insulindependent diabetes mellitus by trans-racial gene mapping the diagnosis and management of kawasaki disease adenovirus infection in patients with kawasaki disease could a herpesvirus be the cause of kawasaki disease? mycoplasma infection and kawasaki disease probable role of streptococcus pyogenes in kawasaki disease serologic evidence that streptococcal superantigens are not involved in the pathogenesis of kawasaki disease variant streptococcus sanguis as an etiological agent of kawasaki disease toxic shock syndrome toxin-secreting staphylococcus aureus in kawasaki syndrome the absence of evidence of staphylococcal toxin involvement in the pathogenesis of kawasaki disease variant strain of propionibacterium acnes: a clue to the etiology of kawasaki disease pathogenicity of propionibacterium acnes isolated from kawasaki disease patients-cytopathogenic protein (cpp) isolated from p. acnes culture filtrates and measurement of the antibody against cpp positive ehrlichia canis serology in kawasaki disease ehrlichia chaffeensis and rochalimaea antibodies in kawasaki disease rickettsia-like bodies and splenitis in kawasaki disease failure to confirm the rickettsial etiology of mcls (kawasaki disease) epstein-barr virus genome-positive tubulointerstitial nephritis associated with kawasaki disease-like coronary aneurysms kawasaki disease, epstein-barr virus and coronary artery aneurysms kawasaki disease and epstein-barr virus the etiology of kawasaki disease: retrovirus? polymerase activity in lymphocyte culture supernatants from patients with kawasaki disease virus-like particles with reverse transcriptase activity associated with kawasaki disease a measles virus isolate from a child with kawasaki disease: sequence comparison with contemporaneous isolates from 'classical' cases isolation of measles virus from child with kawasaki disease demonstration of chlamydia pneumoniae in cardiovascular tissues from children with kawasaki disease is there an association between kawasaki disease and chlamydia pneumoniae failure to demonstrate chlamydia pneumoniae in cardiovascular tissue from children with kawasaki disease is kawasaki disease a variant of q fever? kawasaki disease in european adult associated with serological response to coxiella burneti role of house dust mites in kawasaki disease urine mercury levels in kawasaki disease rug shampoo and kawasaki disease association of rug shampooing and kawasaki disease clinical and epidemiologic characteristics of patients referred for evaluation of possible kawasaki disease. united states multicenter kawasaki disease study group the authors' kawasaki key: cord-262017-utvy0i8l authors: tobar vega, pool; erramilli, shruti; lee, eugene title: talaromyces marneffei laboratory cross reactivity with histoplasma and blastomyces urinary antigen date: 2019-06-21 journal: int j infect dis doi: 10.1016/j.ijid.2019.06.018 sha: doc_id: 262017 cord_uid: utvy0i8l talaromyces marneffei is a fungal opportunistic infection usually seen in immunocompromised patients from eastern countries. in the us when examining hiv-patients for suspected fungal infections, laboratory serological tests guide therapy until cultures are available. we present the case of a 35-year-old hiv patient originally from thailand in which urine lab results were positive for blastomyces and histoplasma antigen, but biopsy showed t. marneffei. concomitantly the patient presented with hyponatremia which was deemed to be from siadh. we present the first case of a patient with t. marneffei cross reactivity with blastomyces, histoplasma and siadh due to pulmonary disease. endemic to southeast asia, east asia and china, talaromyces marneffei is a dimorphic fungus capable of causing systemic fungal infections in immunocompromised patients (supparatpinyo et al., 1994) . since its discovery in the 1950s, the majority of cases have been documented in hiv patients with low cd4 counts. in northern thailand, t. marneffei is the fourth most prevalent opportunistic infection in this population (chariyalertsak et al., 2001) . clinical manifestations include fever, malaise, lymphadenopathy, cough, and hepatosplenomegaly (wu et al., 2008) . while the frequency of t. marneffei infection has decreased with the advent of retroviral therapy, if left untreated the infection frequently leads to respiratory failure with a poor prognosis. in the u.s. patients with hiv infection usually undergo testing for endemic fungal infections such as blastomyces, histoplasma, coccidioides and paracoccidioides. indirect serological results help to make faster decisions given that cultures take several days or weeks to grow. clinical and geographic context plays a particularly important role because some of these tests have been shown to have cross-reactivities. pulmonary infection either by fungi, bacteria or virus has been observed to cause concomitant hyponatremia, with inappropriate levels of antidiuretic hormone (siadh) often found as the underlying etiology. the exact mechanism is not understood but hypoxemia and hypercapnia are thought to play an important role in the pathophysiology (rose et al., 1984) . in the following, we describe a t. marneffei infection with unusual laboratory and clinical characteristics. the patient was a 35-year-old male from thailand who presented with generalized weakness and fever. his past medical history was relevant for hiv infection (since age 21) on haart (bictegravir, emtricitabine & tenofovir alafenamide). two weeks prior to his admission, he had travelled to chicago, las vegas and utah. during this time, he developed a productive cough with blood-tinged sputum, subjective fever, chills, and anorexia with associated weight loss. on physical exam, he was noted to have multiple erythematous, raised, scaly/crusted lesions on the face, neck and abdomen (figure 1 hiv viral load was 3.12 * 10 6 copies/ml and cd4 count was 8 cells/ml. right upper quadrant ultrasound revealed hepatomegaly and a chest x-ray reported bilateral peri-tracheal soft densities up to 3 cm in diameter, interstitial markings, and bilateral pulmonary nodules. chest ct scan without contrast showed patchy pulmonary densities and multiple peri-hilar nodules ( figure 2 ). ct scan with contrast of the head and neck did not reveal acute intracranial abnormalities but did show cervical lymphadenopathy. gram stain smear and culture of the sputum were negative. respiratory viral panel including influenza, parainfluenza, coronavirus and rsv was negative. legionella urine antigen was negative. bacterial blood cultures and gram stain were negative. quantiferon gold and three sputum samples for afb/culture were negative for tuberculosis. serological testing for cryptococci and blastomyces were negative. however, urine antigen testing for both blastomyces and histoplasma were positive. finally, a biopsy of one of the cutaneous lesions demonstrated dermal and subcutaneous neutrophil and histiocyte infiltrate with the presence of intracellular yeast, findings which were consistent with t. marneffei. t. marneffei infections typically manifest in severely immunocompromised patients. current guidelines recommend that in hiv patients from endemic countries with a cd4 count <100 cells/ml, primary preventive therapy with itraconazole should be initiated (panel on opportunistic infections in hiv-infected adults and adolescents, 2019). clinical manifestations appear to vary depending on the severity and underlying etiology of immune compromise in the patient, differing between hiv vs. non-hiv causes such as malignancies or transplant patients. fever, splenomegaly, anemia, transaminitis, and absence of leukocytosis seem to be more frequently found in hiv-positive patients (kawila et al., 2013) . in our case, clinical findings included fever, neck lymphadenopathy, and respiratory symptoms. laboratory work demonstrated transaminitis along with a cd4 count of 8 cells/ml. an initial laboratory test for endemic fungi can guide initial treatment towards early antifungal medication. however, crossreactivity between antigens in various fungal infection detection tests is well-documented, and cross reactions between histoplasma and blastomyces antigens are the most common (wheat et al., 1986) . others have been described, such as that of histoplasma antigen in patients with sporotrichosis (assi et al., 2011) . in our case, urine antigen testing results for both histoplasma and blastomyces were positive, serum testing was negative. it is of note that the sensitivities of the blastomyces and histoplasma antigen detection test in urine are approximately 80% and 89% respectively. specificity is around 90% for both tests, usually having to rule out each other as the main confounder (cunningham et al., 2015; frost and novicki, 2015) . hiv status can affect tests based on antibody detection. since the tests used to guide therapy are based on antigen detection, sensitivity is unlikely to be affected by hiv infection. these infections in their disseminated forms will receive amphotericin-b with itraconazole. however, differentiation is important given that blastomycosis is treated for a year versus talaromyces which is treated for 12 weeks (sirisanthana et al., 1998; saccente and woods, 2010) . siadh is an exclusion diagnosis that requires an extensive work up to rule out other etiologies including adrenal insufficiency, thyroid disease, and volume depletion (shu et al., 2018) . adh is produced on the paraventricular thalamic nucleus and thus classically this syndrome is observed after neurological insults that cause an excess in adh. nevertheless, it has been observed that respiratory tract infections can cause inadequate adh secretion and these are the most common infections in hiv patients. increase in the a-a gradient and hypoxia/hypercapniainduced adh secretion are some of the non-osmotic mechanisms thought to trigger elevations in adh in this population. it has been proposed that hypercapnic acidosis and hypoxemia induce central release of vasopressin through peripheral chemoreceptors and baroreceptors stimulation respectively (rose et al., 1984; dreyfuss et al., 1988) . tuberculosis, cryptosporidium, plasmodium infections and pneumocystis pneumonia have been previously reported as pulmonary infections causing siadh. it is of note that hiv by itself could contribute to siadh. but the mechanism underlying this infection is usually mediated by hiv induced thyroid and adrenal insufficiency. in our case, the patient had increased urinary sodium, decreased serum osmolality, normal cortisol and tsh levels and absence of neurological affect, leaving the pulmonary fungal infection as one of the explanations for inadequate adh secretion. in conclusion, laboratory work up for endemic fungal infection can have false positive results with infections such as talaromyces. this cross reactivity is especially important when assessing patients from endemic countries. manifestations of t. marneffei infection are diverse, and disease description is limited due to the small number of cases. a novel manifestation observed in our patient was the presence of siadh likely secondary to the respiratory talaromyces infection. to our knowledge, this is the first case reporting systemic mycosis due totalaromyces marneffei with associated hyponatremia secondary to siadh and cross-reactivity with blastomyces and histoplasma in urine antigen testing. cross-reactivity in the histoplasma antigen enzyme immunoassay caused by sporotrichosis clinical presentation and risk behaviors of patients with acquired immunodeficiency syndrome in thailand, 1994-1998: regional variation and temporal trends sensitivity and specificity of histoplasma antigen detection by enzyme immunoassay acute infectious pneumonia is accompanied by a latent vasopressin-dependent impairment of renal water excretion blastomyces antigen detection for diagnosis and management of blastomycosis panel on opportunistic infections in hiv-infected adults and adolescents. guidelines for the prevention and treatment of opportunistic infections in hiv-infected adults and adolescents: recommendations from the centers for disease control and prevention, the national institutes of health, and the hiv medicine association of the infectious diseases society of america antidiuresis and vasopressin release with hypoxemia and hypercapnia in conscious dogs clinical and laboratory update on blastomycosis hiv/aids-related hyponatremia: an old but still serious problem amphotericin b and itraconazole for treatment of disseminated penicillium marneffei infection in human immunodeficiency virus-infected patients disseminated penicillium marneffei infection in southeast asia evaluation of cross-reactions in histoplasma capsulatum serologic tests clinical presentations and outcomes of penicillium marneffei infections: a series from aknowledgement is given to dr saad, peguy who proof read this manuscript. consent was obtained from patient for the publication of this manuscript.consent was obtained from patient for the publication of this manuscript. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. the authors declare no conflict of interest. key: cord-254872-w6d397js authors: stein, richard a. title: methicillin-resistant staphylococcus aureus—the new zoonosis date: 2008-11-30 journal: int j infect dis doi: 10.1016/j.ijid.2008.09.008 sha: doc_id: 254872 cord_uid: w6d397js nan the etiologic agents of many emerging infectious diseases are thought to originate in animal reservoirs 1 and, after becoming established in the human population, to spread by direct human-to-human contact. the crossing of species barriers is historically credited with some of the most devastating and unconventional outbreaks, and pandemic influenza, creutzfeldt-jacob disease, west nile virus, severe acute respiratory syndrome (sars), and hiv represent some of the notable examples still vivid in public memory. [1] [2] [3] [4] one of the major public health crises we are currently witnessing is the one linked to methicillin-resistant staphylococcus aureus (mrsa). while mrsa is easily transmitted among humans by direct skin-to-skin contact, by contact with infected biological material or contaminated personal objects, or through the airborne route, food-initiated outbreaks are increasingly implicated in human infections. 5 several reports reveal that this pathogen can be isolated from cattle, pig, and chicken samples in slaughterhouses 6 and from food samples randomly tested in supermarkets. 7, 8 at the same time, a thought-provoking phenomenon is currently unraveling. although mrsa has historically been associated with healthcare and has become known as hospital-associated mrsa, it increasingly emerges without relationship to healthcare, in patients without apparent risk factors, as a distinct epidemiological, microbiological, and clinical entity known as community-associated mrsa. 9,10 the prevalence of community-associated mrsa, as revealed by a recent study conducted on 2636 patients with skin and skin structure s. aureus infections, increased from 9% in 2004 to 16% in 2005 and 21% in 2006. 11 at the same time, growing epidemiological and genetic evidence points towards mrsa transmission across species, and unveils a previously unknown face that this microorganism is assuming, as an emerging zoonotic pathogen. the surge in community-associated mrsa, at a time when reports of animal-to-human transmission are increasing, might not be merely coincidental, 12, 13 and according to a recent study conducted in the netherlands, mrsa that entered from an animal reservoir into the human population is now responsible for over 20% of the strains isolated. 14 findings that have accumulated in recent years make it necessary to define three additional patient groups at high risk for zoonotic mrsa: individuals in contact with farm animals, contacts of household pets, and veterinarian staff. in 2003, a new non-typeable mrsa strain was identified in the netherlands and linked to animal farming; subsequent studies supported the possibility of farm workers becoming infected from farm animals. [14] [15] [16] [17] [18] [19] non-typeability with sma i by pulsed field gel electrophoresis has emerged over the years as a shared characteristic of mrsa strains originating in pigs, 20 and currently over 39% of slaughterhouse pigs in the netherlands are estimated to be positive for non-typeable mrsa isolates. 21 in the netherlands, 23% of pig farmers 19 and 32% of farm workers exposed to pigs and veal calves 17 were found to be colonized with mrsa, rates that exceed 760 and 1000 times, respectively, those seen in the general population, and that outweigh those reported for any other population described so far. a similar study conducted among pig farmers in north america found colonization rates of 20%, 22 supporting the possibility that pigs represent reservoirs for human mrsa infections irrespective of the geographic area. moreover, it is important to note that mrsa strains of animal origin have been isolated from people lacking previous documented direct animal contacts, supporting the possibility that direct human-to-human transmission occurs subsequent to one person's colonization/infection. after a female patient was diagnosed with mrsa mastitis, 18 her farmer husband, their baby girl, and three co-workers from the same farm were found to be colonized, as were eight out of 10 randomly chosen pigs. the strain isolated from the baby was genetically identical to the one isolated from her parents, 18 despite her lack of direct contact with farm animals. in another example, mrsa was found in the screening cultures of a 6-month-old girl before thoracic surgery, and subsequently her parents were found to be colonized as well, presumably from a pig that the family raised on the farm. 19 mrsa transmission also occurs, in both directions, between humans and household animals. owners have been shown to infect pets, and these pets may subsequently act as reservoirs to infect and/or re-infect susceptible hosts. 13 several studies underscore the possibility of pet dogs colonizing household contacts. 13, [23] [24] [25] a diabetic patient and his wife exhibited recurrent mrsa leg infections and cellulitis, respectively, and both were cured only after their dog was treated as well. 25 remarkably, mrsa was isolated from a kitten for up to 9 months after the initial diagnosis, an alarming finding that points towards the possibility of prolonged colonization of pets and the subsequent increased risk of transmission to household members. 13 veterinary clinic personnel represent the third group at risk for mrsa colonization and/or infection. very similar mrsa strains have been isolated from animals and animal care staff. 26 as recently pointed out, 27 mrsa carriage is significantly higher (3.9% vs. 0.7%) among veterinary practitioners than among individuals without professional exposure to animals. the screening of 80 veterinary students and 99 veterinarians in the netherlands 28 revealed a 4.6% prevalence of mrsa carriage in this group, while other surveys performed on international veterinary conference attendees have reported mrsa colonization rates of 6.5%, 29 10.1%, 30 and 12.5%, 31 values that exceed, by far, mrsa prevalence in the general population, estimated to range between 0.03% and 3%. [32] [33] [34] professionals with frequent animal contact (daily or 5 hours/week) were found to have the highest risk for colonization. however, as revealed by a recent study on personnel working with neonatal horses, contacts as short as 4 hours are sufficient for the infection of veterinary personnel. 12 these findings have prompted the suggestion that veterinary personnel, when managing skin and skin-related soft tissue mrsa infections, should always consider previous contacts with animals. 12 in the context of these findings, the defining of additional groups at high risk for mrsa colonization and infection emerges as an urgent task. recent hospitalizations, outpatient visits, nursing home admissions, antibiotic exposure, chronic illness, and injection drug use are some of the most important mrsa risk factors. 34, 35 however, maintaining a high index of suspicion in animal farmers and their families, pet owners, and professionals involved in animal care is essential, particularly when no apparent risk factors can be identified or when infections recur despite initial successful treatment. moreover, besides the medical aspect, it is important to reflect on the broader public health perspective. zoonotic colonization of these high-risk groups can provide the initial mrsa port of entry into the human population, facilitating subsequent direct human-to-human transmission--an alarming scenario, especially if we recall the h5n1 influenza virus, for which human-to-human transmission was proposed to represent the last barrier needed to unleash a pandemic. 36 host species barriers to influenza virus infections catastrophes after crossing species barriers emerging zoonoses: crossing the species barrier influenza as a model system for studying the crossspecies transfer and evolution of the sars coronavirus food-initiated outbreak of methicillin-resistant staphylococcus aureus analyzed by pheno-and genotyping methicillin (oxacillin)-resistant staphylococcus aureus strains isolated from major food animals and their potential transmission to humans characterization of methicillin-resistant staphylococcus aureus isolated from retail raw chicken meat in japan methicillin-resistant staphylococcus aureus (mrsa) in foods of animal origin product in italy community-associated mrsa (ca-mrsa): an emerging pathogen in infective endocarditis proposed definitions of community-associated methicillin-resistant staphylococcus aureus (ca-mrsa) trends in prescribing b-lactam antibiotics for treatment of communityacquired methicillin-resistant staphylococcus aureus infections an outbreak of methicillin-resistant staphylococcus aureus skin infections resulting from horse to human transmission in a veterinary hospital suspected transmission of methicillin-resistant staphylococcus aureus between domestic pets and humans in veterinary clinics and in the household emergence of methicillin-resistant staphylococcus aureus of animal origin in humans clonal comparison of staphylococcus aureus isolates from healthy pig farmers, human controls, and pigs antimicrobial resistance in pig faecal samples from the netherlands (five abattoirs) and sweden increase in a dutch hospital of methicillin-resistant staphylococcus aureus related to animal farming community-acquired mrsa and pig-farming methicillinresistant staphylococcus aureus in pig farming presence of a novel dna methylation enzyme in methicillin-resistant staphylococcus aureus isolates associated with pig farming leads to uninterpretable results in standard pulsed-field gel electrophoresis analysis high prevalence of methicillin-resistant staphylococcus aureus in pigs methicillin-resistant staphylococcus aureus colonization in pigs and pig farmers human carriage of methicillinresistant staphylococcus aureus linked with pet dog human-to-dog transmission of methicillin-resistant staphylococcus aureus asymptomatic nasal carriage of mupirocin-resistant, methicillin-resistant staphylococcus aureus (mrsa) in a pet dog associated with mrsa infection in household contacts methicillin-resistant staphylococcus aureus (mrsa) isolated from animals and veterinary personnel in ireland high risk for nasal carriage of methicillin-resistant staphylococcus aureus among danish veterinary practitioners methicillin-resistant staphylococcus aureus in veterinary doctors and students, the netherlands methicillin-resistant staphylococcus aureus colonization in veterinary personnel evaluation of prevalence and risk factors for methicillin-resistant staphylococcus aureus colonization in veterinary personnel attending an international equine veterinary conference mrsa in livestock animals--an epidemic waiting to happen? low prevalence of methicillin resistant staphylococcus aureus (mrsa) at hospital admission in the netherlands: the value of search and destroy and restrictive antibiotic use natural history of community-acquired methicillin-resistant staphylococcus aureus colonization and infection in soldiers community-acquired methicillin-resistant staphylococcus aureus: prevalence and risk factors community-acquired methicillin-resistant staphylococcus aureus: a meta-analysis of prevalence and risk factors influenza virus transmission: basic science and implications for the use of antiviral drugs during a pandemic key: cord-255021-acgfwjwi authors: luo, ying; yuan, xu; xue, ying; mao, liyan; lin, qun; tang, guoxing; song, huijuan; liu, weiyong; hou, hongyan; wang, feng; sun, ziyong title: using the diagnostic model based on routine laboratory tests to distinguish patients infected with sars-cov-2 from those infected with influenza virus date: 2020-05-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.078 sha: doc_id: 255021 cord_uid: acgfwjwi abstract background the differential diagnosis between novel coronavirus pneumonia patients (ncpp) and influenza patients (ip) remains a challenge in clinical practice. methods between january 2018 and march 2020, 1027 ncpp and 1140 ip were recruited from tongji hospital. blood routine examination, biochemical indicators, and coagulation function analysis were performed in all participants simultaneously. results there was no sex predominance in ncpp. the ncpp were frequently encountered in the sixth and seventh decades of life. the mean age of ncpp (56±16 years) was higher than ip (47±17 years), but without statistical difference. although most results of routine laboratory tests between ncpp and ip had no significant difference, some laboratory tests showed an obvious change in ncpp. we observed that ncpp had significantly decreased white blood cells, alkaline phosphatase, and d-dimer, compared with ip. however, the results of lactate dehydrogenase, erythrocyte sedimentation rate and fibrinogen were significantly increased in ncpp compared with those in ip. the diagnostic model based on combination of eighteen routine laboratory indicators showed an area under the curve of 0.796 (95% ci, 0.777 to 0.814), with a sensitivity of 46.93% and a specificity of 90.09% when using a cutoff value of 0.598. conclusions some routine laboratory results had statistical difference between ncpp and ip. a diagnostic model based on combination of routine laboratory results provides an adjunct approach in the differential diagnosis between ncpp and ip. there was no sex predominance in ncpp. the ncpp were frequently encountered in 33 the sixth and seventh decades of life. the mean age of ncpp (56±16 years) was 34 higher than ip (47±17 years), but without statistical difference. although most results 35 of routine laboratory tests between ncpp and ip had no significant difference, some 36 laboratory tests showed an obvious change in ncpp. we observed that ncpp had 37 significantly decreased white blood cells, alkaline phosphatase, and d-dimer, the lancet, 2020). more than 87,000 individuals have been confirmed infected with 71 the virus in china as of march 1, 2020 and most cases were reported in wuhan city. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. in total, 1027 ncpp and 1140 ip were recruited from tongji hospital between january 166 2018 and march 2020. the demographic information was summarized in table 1 . 167 there was no sex predominance in ncpp. rdw-sd, standard deviation in red cell distribution width; plt#, platelet count; pdw, platelet distribution width; mpv, mean platelet volume; plcr, platelet larger cell ratio; thr, thrombocytocrit. *comparisons were performed between ncpp and ip groups using mann-whitney u test. data were presented as medians (25th-75th percentages). variables ncpp (n=1027) ip (n=1140) p* genomic characterization of 304 the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical 305 pneumonia after visiting wuhan epidemiological and clinical 307 characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a 308 descriptive study return of the coronavirus: 2019-ncov clinical features of patients 312 infected with 2019 novel coronavirus in wuhan an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice key: cord-288167-976qxja2 authors: park, wan beom; poon, leo l.m.; choi, su-jin; choe, pyoeng gyun; song, kyoung-ho; bang, ji hwan; kim, eu suk; kim, hong bin; park, sang won; kim, nam joong; peiris, malik; oh, myoung-don title: replicative virus shedding in the respiratory tract of patients with middle east respiratory syndrome coronavirus infection date: 2018-05-09 journal: int j infect dis doi: 10.1016/j.ijid.2018.05.003 sha: doc_id: 288167 cord_uid: 976qxja2 background: information on the duration of replicative middle east respiratory syndrome coronavirus (mers-cov) shedding is important for infection control. the detection of mers-cov sub-genomic mrnas indicates that the virus is replicative. this study examined the duration for detecting mers-cov sub-genomic mrna compared with genomic rna in diverse respiratory specimens. methods: upper and lower respiratory samples were obtained from 17 mers-cov-infected patients. mers-cov sub-genomic mrna was detected by reverse transcription pcr (rt-pcr) and mers-cov genomic rna by real-time rt-pcr. results: in sputum and transtracheal aspirate, sub-genomic mrna was detected for up to 4 weeks after symptoms developed, which correlated with the detection of genomic rna. in oropharyngeal and nasopharyngeal swab specimens, the detection of sub-genomic mrna and genomic rna did not correlate. conclusions: these findings suggest that mers-cov does not replicate well in the upper respiratory tract. middle east respiratory syndrome coronavirus (mers-cov) genomic rna can persist for more than 1 month in respiratory specimens (memish et al., 2014) . however, the detection of mers-cov rna may overestimate the duration of shedding of replicative virus. coronaviruses have a unique mechanism of discontinuous transcription with the synthesis of sub-genomic mrnas (sawicki et al., 2007) . the mers-cov has at least seven distinct sub-genomic mrna species and the detection of these indicates that the virus is replicative (woo et al., 2016) . the objectives of this study were to examine the duration for detecting mers-cov sub-genomic mrna vs. genomic rna in different respiratory specimens. respiratory samples were collected from 17 patients admitted to three seoul national university (snu) affiliated hospitals during the 2015 mers outbreak in korea. the patients were categorized into severe (a-i) or mild (j-q) groups depending on their oxygen supplementation requirements. the severe group required oxygen supplementation to maintain arterial saturation above 90%. patients a-e received ventilator therapy, while patients f-i did not (park et al., 2015) . the institutional review board at snu hospital provided study approval and waived the requirement for written consent. oropharyngeal and nasopharyngeal swabs were collected using a utm kit containing viral transport medium (copan diagnostics inc., murrieta, ca, usa). the rna was extracted from respiratory samples using a qiaamp viral rna mini kit (qiagen, valencia, ca, usa). to detect the mers-cov genomic rna, multiplex quantitative real-time reverse transcription (rrt)-pcr was performed using the powerchek mers (upe & orf1a) real-time pcr kit (kogenebiotech, seoul, south korea) and all assays were performed using a viia7 real-time pcr system (applied biosystems, grand island, ny, usa). the results of genomic rna titers have been presented in part in a previous publication (oh et al., 2016) . the mers-cov sub-genomic mrna was detected using accu-power rt-pcr premix (binder inc., alameda, ca, usa). pcr primers were designed to detect sub-genomic mrna that codes for the spike (s) (433 bp) and nucleocapsid (n) (662 bp) proteins (table 1) . forward primer was elaborated from the leader sequence and backward primers of 5 0 untranslated region (utr)-s and 5 0 utr-n were from gene sequences coding for proteins s and n, respectively. the pcr reactions were performed as follows: initial denaturation at 94 c for 5 min and 40 cycles of denaturation at 94 c for 20 s, annealing at 55 c for 30 s, and extension at 72 c for 1 min. sub-genomic mrna was sequenced using a dna engine tetrad 2 peltier thermal cycler (bio-rad) and the abi bigdye terminator v3.1 cycle sequencing kit (applied biosystems, grand island, ny, usa). if the sequences included the leader sequence and were consistent with the mers-cov genome by 98% using basic local alignment search tool (blast) software, they were confirmed as sub-genomic mrna. in sputum and transtracheal aspirates, the detection of mers-cov sub-genomic mrna was more frequent in the severe group than in the mild group ( figure 1a ). sub-genomic mrna was detected 28 days after the illness onset. in the severe group, the period for detecting sub-genomic mrna strongly correlated with the duration for detecting mers-cov genomic rna (pearson correlation coefficient = 0.803, p = 0.009). the mers-cov genomic rna titer was significantly higher in the specimens with subgenomic mrna detection than in those where sub-genomic mrna was not detected (p = 0.0007) (figure 2 ). in oropharyngeal swab specimens, sub-genomic mrna was detected only in the severe group for up to 11 days after the illness onset ( figure 1b) , and the period for detecting sub-genomic mrna was not significantly correlated with that for mers-cov genomic rna (pearson correlation coefficient = 0.335, p = 0.378). no subgenomic mrna was detected in nasopharyngeal swab specimens ( figure 1c ). in the present study, replicative mers-cov was detected in sputum or transtracheal aspirate for up to 4 weeks after symptom development in mers-cov-infected patients with severe pneumonia. this result is consistent with the findings of previous studies that have tested mers-cov genomic rna (memish et al., 2014; corman et al., 2016; min et al., 2016) . on the basis of these results, infection prevention and control precautions should be thoroughly applied for at least 1 month after symptom onset if the patient with mers-cov infection has severe pneumonia. the differences in the detection of replicative viruses between upper and lower respiratory tract specimens may have originated from differences in viral titers. several studies have demonstrated that the viral titer of mers-cov rna in upper respiratory tract specimens is lower than that in lower respiratory tract specimens (oh et al., 2016; corman et al., 2016) . in the present study, subgenomic mrna was not detected in any of the nasopharyngeal specimens. the current guidelines recommend that isolation should continue until two consecutive upper respiratory tract specimens taken at least 24 h apart test negative by rt-pcr (who, 2018) . however, the present study suggests that, if possible, lower respiratory tract specimens should be used to determine the duration of isolation and that nasopharyngeal swab specimens should be avoided. this study has a few limitations. first, differences in sensitivity between the real-time rt-pcr used to detect genomic rna and the conventional rt-pcr for sub-genomic mrna may have affected the results. second, rt-pcr methods for sub-genomic mrna have not been validated elsewhere. other methods, such as detecting live virus, should be performed to validate the methods used in this study. in conclusion, replicative mers-cov was detected in lower respiratory tract specimens for up to 4 weeks after symptom development, which was well correlated with the detection of genomic rna. in upper respiratory tract specimens, the detection of sub-genomic mrna and genomic rna did not correlate. these findings suggest that mers-cov does not replicate well in the upper respiratory tract. viral shedding and antibody response in 37 patients with middle east respiratory syndrome coronavirus infection middle east respiratory syndrome coronavirus (mers-cov) viral shedding in the respiratory tract: an observational analysis with infection control implications comparative and kinetic analysis of viral shedding and immunological responses in mers patients representing a broad spectrum of disease severity kinetics of serologic responses to mers coronavirus infection in humans a contemporary view of coronavirus transcription management of asymptomatic persons who are rt-pcr positive for middle east respiratory syndrome coronavirus (mers-cov). interim guidance isolation and characterization of dromedary camel coronavirus uae-hku 23 from dromedaries of the middle east: minimal serological cross-reactivity between mers coronavirus and dromedary camel coronavirus uae-hku 23 middle east respiratory syndrome coronavirus (mers-cov) genomic rna (upe) titers in sputum and transtracheal aspirates with vs. without sub-genomic mrna detection. solid lines indicate the mean and standard error of the mean none. key: cord-268599-z54p3dk3 authors: panda, swagatika; mohakud, nirmal kumar; pena, lindomar; kumar, subrat title: human metapneumovirus: review of an important respiratory pathogen date: 2014-05-17 journal: int j infect dis doi: 10.1016/j.ijid.2014.03.1394 sha: doc_id: 268599 cord_uid: z54p3dk3 human metapneumovirus (hmpv), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immune-compromised patients. hmpv is the major etiological agent responsible for about 5% to 10% of hospitalizations of children suffering from acute respiratory tract infections. hmpv infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. initial infection with hmpv usually occurs during early childhood, but re-infections are common throughout life. due to the slow growth of the virus in cell culture, molecular methods (such as reverse transcriptase pcr (rt-pcr)) are the preferred diagnostic modality for detecting hmpv. a few vaccine candidates have been shown to be effective in preventing clinical disease, but none are yet commercially available. our understanding of hmpv has undergone major changes in recent years and in this article we will review the currently available information on the molecular biology and epidemiology of hmpv. we will also review the current therapeutic interventions and strategies being used to control hmpv infection, with an emphasis on possible approaches that could be used to develop an effective vaccine against hmpv. acute respiratory tract infection (ari) is a leading cause of morbidity and mortality worldwide. globally, aris were responsible for about 20% of total deaths in children less than 5 years of age in 2000 alone; moreover, about 70% of these deaths occurred in sub-saharan africa and the southern regions of asia. 1 aris affect children regardless of their economic status, with similar incidence rates in both developed and developing countries, but with a higher mortality rate in developing countries. 2 the risk of pneumonia is higher in children in developing countries (10-20%, compared to 3-4% in developed countries). 3 a wide range of etiological agents are responsible for respiratory problems in children. 4 although upper respiratory tract infections are generally less serious, they nonetheless carry significant societal costs in terms of lost work, lost school days, and additional health care costs. for this reason, determining the etiological agents of these infections is important. with decades of research and epidemiological studies, we have been able to establish the importance of known viral pathogens like human respiratory syncytial virus (hrsv), parainfluenza virus, influenza virus, coronavirus, and rhinovirus. however, despite these studies, a substantial proportion of respiratory tract infections still cannot be attributed to any known pathogen. human metapneumovirus (hmpv) was first discovered in 2001 in the netherlands, when the virus was isolated from a paediatric patient who had symptoms similar to those of hrsv infection. 5 since then, hmpv has been detected in 4-16% of patients with aris. [6] [7] [8] the incidence of hmpv may vary from year to year in the same area. 9 hmpv causes disease primarily in children, but can infect adults and immunocompromised individuals as well. the clinical features of the illness caused by hmpv infection range from a mild upper respiratory tract infection to life-threatening severe bronchiolitis and pneumonia. human metapneumovirus (hmpv), discovered in 2001, most commonly causes upper and lower respiratory tract infections in young children, but is also a concern for elderly subjects and immunecompromised patients. hmpv is the major etiological agent responsible for about 5% to 10% of hospitalizations of children suffering from acute respiratory tract infections. hmpv infection can cause severe bronchiolitis and pneumonia in children, and its symptoms are indistinguishable from those caused by human respiratory syncytial virus. initial infection with hmpv usually occurs during early childhood, but re-infections are common throughout life. due to the slow growth of the virus in cell culture, molecular methods (such as reverse transcriptase pcr (rt-pcr)) are the preferred diagnostic modality for detecting hmpv. a few vaccine candidates have been shown to be effective in preventing clinical disease, but none are yet commercially available. our understanding of hmpv has undergone major changes in recent years and in this article we will review the currently available information on the molecular biology and epidemiology of hmpv. we will also review the current therapeutic interventions and strategies being used to control hmpv infection, with an emphasis on possible approaches that could be used to develop an effective vaccine against hmpv. belonging to the order mononegavirales, the paramyxoviridae family is divided into the subfamilies paramyxovirinae and pneumovirinae. the pneumovirinae subfamily is further divided into two genera, pneumovirus and metapneumovirus. hrsv is placed under the genus pneumovirus, while hmpv is placed under the genus metapneumovirus. whole genome analysis has shown that hmpv exists as two genotypes, a and b. based upon the sequence variability of the attachment (g) and fusion (f) surface glycoproteins, these two genotypes are further divided into subgroups a1, a2, b1, and b2. subgroup a2 is again subdivided into a2a and a2b. 10, 11 one study has described a strain that is under major subgroup a, but does not fall into subgroups a1 or a2, and hence there may be a new subgroup evolving in the a major subgroup. 12 study of the molecular biology of hmpv advanced significantly with the establishment of reverse genetics platforms, but we still lack a reliable vaccine to control hmpv infection. recent findings in hmpv molecular virology, diagnosis, and control strategies are reviewed here. the hmpv virion is pleomorphic in nature and its size varies from 150 nm to 600 nm. 5 the genomic orientation of hmpv resembles other members of the paramyxoviridae family ( figure 1 ). the genome organization of hmpv is quite similar to that of avian pneumovirus (ampv), particularly type c. the genomes of hmpv and hrsv closely resemble each other, excluding a few differences in the order of the genes and the absence of the non-structural genes from the hmpv genome ( figure 2 ). for hrsv, the two nonstructural proteins (ns1 and ns2) have been identified as potent multifunctional antagonists of the interferon (ifn) signalling pathways. 13 the absence of these proteins may be the reason for the difference in level of host innate immune response observed during hrsv and hmpv infections. 14 the hmpv genome is comprised of negative-sense single-stranded rna and contains eight genes that code for nine proteins. the order of the genes in the genome (from 3 0 to 5 0 end) is n-p-m-f-m2-sh-g-l. the proteins are: the nucleoprotein (n protein), the phosphoprotein (p protein), the matrix protein (m protein), the fusion glycoprotein (f protein), the putative transcription factor (m2-1 protein), the rna synthesis regulatory factor (the m2-2 protein), the small hydrophobic glycoprotein (sh protein), the attachment glycoprotein (g protein), and the viral polymerase (l protein). 15 the rna core is surrounded by m protein and covered by a lipid envelope. this envelope contains the three surface glycoproteins (f, sh, and g), in the form of spikes of approximately 13-17 nm. the core nucleic acids are associated with the p, n, l, m2-1, and m2-2 proteins and form a nucleocapsid 17 nm in diameter. with the help of the g and f proteins, hmpv attaches and fuses to heparan sulphate receptors on the cell surface. after the fusion process, the viral nucleocapsid enters into the cytoplasm of the host cell and undergoes replication. the newly synthesized viral genome assembles with the viral p, n, l, and m2 proteins, and moves towards the host cell membrane. the virion now buds out of the cell, with the f, sh, and g proteins exposed on the outer side of the membrane. 16, 17 the p protein acts as a co-factor to stabilize the l protein, allowing the formation of the virus ribonucleoprotein (rnp) complex during virus replication. the m protein plays a crucial role in virus assembly and budding by interacting with the rnp complex. the n protein encapsidates the viral genome and protects it from nuclease activity. in addition to regulating viral transcription and replication, the m2-2 protein plays a major role in virulence by decreasing the host's innate immunity. 18, 19 like other members of the paramyxoviridae family, hmpv interferes with the host's innate immune system using specific mechanisms. the virus antagonizes cellular responses by regulating pattern recognition receptors, such as toll-like receptor and retinoic acid-inducible gene-like receptors and other signalling molecules. 20 infection interferes with dendritic cell activity and reduces antigen-specific t cell activation. 21 thus, virus clearance remains incomplete and the chances of re-infection occurring increase. members of the two genotypes show much less amino acid and nucleotide similarity (nucleotide 84-86%, amino acid 94-97%) than members of the same subgroup (a1 and a2, or b1 and b2) within the same genotype (nucleotide 94-96%, amino acid 97-99%) based on the f gene sequence. 8 comparing all the subgroups (a1, a2, b1, and b2), the n gene is found to be most conserved at both the nucleotide and the amino acid levels (91.2% and 98.4%, respectively), while the g gene is the least conserved (79% and 59.2%, respectively). 22 hmpv has been isolated on all continents and has a seasonal distribution. the geographic distribution of the various hmpv genotypes is given in figure 3 . outbreaks occur mainly in the spring and winter months -january to march in the northern hemisphere and june to july in the southern hemisphere. 23, 24 a recent study reported that the peak of the hmpv seasonal cases is observed between march and april following the rsv and influenza infection seasons. 25 another study reported that the hmpv infection season overlaps with that of the rsv infection season. 26 being a respiratory infection, hmpv is transmitted by infectious airborne droplets. 27 seroprevalence studies have shown that a high percentage (90-100%) of children have been infected by the time they are 5-10 years old, but re-infection can occur throughout adulthood. 5 this may be due to insufficient immunity acquired during the initial infection and/or due to infection by different viral genotypes. the incubation period varies from individual to individual, but is commonly between 3 and 5 days. during animal experimentation, peak viral titres are seen between days 4 and 5 in balb/c mice and cotton rats. 28 hmpv is commonly found in the paediatric population, with high susceptibility rates in children less than 2 years old. hmpv infection in adults normally shows only mild flu-like symptoms. however, in some adult cases (especially elderly adults), severe complications such as chronic obstructive pulmonary disease (copd) can occur. 29 dyspnoea is more likely in adults as compared to children. 30 hmpv infection has also been reported in several immunocompromised patients, such as lung transplant recipients, patients with haematological malignancies, and hematopoietic stem cell transplant recipients. 31, 32 two studies found that both genotypes of hmpv (a and b) co-circulated during a typical respiratory virus season, 12, 33 and frequent re-infections with different hmpv genotypes occur. 34 risk factors associated with severe hmpv infection include premature birth, young age, pre-existing nosocomial infection, and underlying chronic pulmonary, heart, or neural disorders. 35 studies investigating the relationship between genotype and disease severity in children have not found any significant correlations. vicente et al. reported that genotype a may be more virulent that genotype b, 36 while papenburg et al. indicated that it was genotype b that was associated with severe hmpv infection. 37 compared to hmpv-negative children, hmpv-infected children were found to be more likely to require supplemental oxygen, to have a longer stay in the intensive care unit (icu), and more likely to have undergone chest radiography. about 40% of children hospitalized with hmpv infection were found to have underlying high risk conditions, like asthma and chronic lung disease. 38 the average annual rate of hospitalization was about three times more in children less than 6 months old (3/1000) compared to children 6 months to 5 years old (1/1000). nosocomial infection has been reported in several studies as a mode of transmission. 39, 40 the annual rate of hospitalization due to hmpv infection is equal to that of influenza and parainfluenza 1, 2, and 3 combined, 38 and a recent analysis of an hmpv outbreak in two skilled nursing facilities showed an 11% mortality rate. 41 the severity of disease caused by this recently discovered virus and the importance of hmpv pathogenesis and vaccine research is now becoming clear. many studies have reported co-infection of hmpv with other respiratory pathogens, including rsv, 42 bocavirus, 23 rhinovirus or enterovirus, parainfluenza virus, 43 coronavirus, 44 influenza a, 45 and influenza b. 46 hmpv co-infection has also been reported during an outbreak of severe acute respiratory syndrome (sars). 47 studies have also found hmpv co-infection with bacterial pathogens like streptococcus pneumoniae, mycoplasma pneumoniae, and chlamydia pneumoniae. 45 however, the interaction of hmpv with these other etiological agents is unclear, as co-infection does not seem to affect hmpv disease severity. 10, 48 there are conflicting reports on the association between rsv-hmpv co-infection and disease severity; some studies found that co-infection leads to an increased rate of icu admission and hospital stay, 49,50 but others found no association between co-infection and disease severity. 51,52 the clinical manifestations of an hmpv infection are indistinguishable from those of an rsv infection, especially in young children. hmpv patients are generally diagnosed with bronchiolitis, bronchitis, and pneumonia. they show common symptoms like fever, cough, hypoxia, upper respiratory tract infection, lower respiratory tract infection, and wheezing. 53 however, the most common causes of hospitalization are bronchiolitis and pneumonia. 54 the average duration of fever in hmpv-positive cases is about 10 days, with a peak during the course of the illness. 55 young adults with hmpv re-infection show mild cold and flu-like symptoms, with fever in a small proportion of infected cases. however, in the case of elderly patients, re-infection can lead to severe symptoms (such as pneumonitis) and even to death. 30 one study reported that 50% of children with hmpv infection were diagnosed with otitis media 56 and another study reported that hmpv infection was found in about 8% of children who came to the hospital with wheezing. 57 wheezing is a common clinical symptom observed in multiple studies of children with hmpvassociated lower respiratory tract infections. 58 hmpv infections can lead to asthma exacerbations in small children and adults. 31 hmpv acts as an enhancer of copd 59 and patients with copd are more prone to hmpv infection. 60 ,61 a few reports have also suggested that hmpv infection in children may be associated with a spectrum of central nervous system diseases ranging from febrile seizures to severe encephalitis. 62 hmpv was detected by real-time rt-pcr in asymptomatic children, but they had significantly lower viral loads that those found in symptomatic children. 63 higher hmpv viral loads were significantly correlated with the course of illness and disease severity, irrespective of genotype. 64 high levels of hmpv viral shedding lasted from 1 to 2 weeks after acute illness. 65, 66 hmpvassociated fatal pneumonia has been indicated in the case of a child receiving chemotherapy for acute lymphoblastic leukemia. 34 hmpv was found to be the sole etiological agent responsible for the fatal infection of an allogeneic haematopoietic stem cell transplant patient showing interstitial and intra-alveolar pneumonitis with profound alveolar cell damage. 32 hmpv infection during the first week after haematopoietic stem cell transplant may be associated with much higher morbidity and mortality rates. 66 hmpv can cause a range of illnesses in lung transplant recipients, from a mild upper respiratory tract infection to a severe lower respiratory tract infection. 67, 68 in a prospective study involving patients with severe motor and intellectual disabilities, the early stages of hmpv infection were characterized by a low to moderate increase in c-reactive protein (crp) levels, reduced peripheral blood lymphocytes, and an elevated monocyte ratio. 55 although the peripheral blood lymphocytes and monocyte ratio normalized with the mitigation of symptoms, the crp levels persisted for some time. 55 along with elevated serum crp levels, a few hospitalized children infected with hmpv were also reported to have leukopenia and leukocytosis. 69 persistent infection by hmpv may be attributed to a minimal and late immune response, as well as delayed cytotoxic tlymphocyte activity with impaired virus clearance during primary infection. 70 hmpv interferes with superantigen-induced t cell activation by infecting dendritic cells. thus, the proliferation of antigen-specific cd4+ t cells is restricted and the production of long-term immunity is impaired. 21 respiratory viruses are known to modulate cytokine responses. compared to rsv and influenza, hmpv is a less effective inducer of different cytokines like interleukin (il)-12, tumour necrosis factor alpha (tnf-a), il-6, il-1b, il-8, and il-10. 71 hmpv infection induces pulmonary inflammatory changes in balb/c mice and cotton rats and leads to an increase in the levels of interleukins (il-2, il-8, il-4), interferon (ifn-a), macrophage inflammatory protein 1a, and monocyte chemotactic proteins in the bronchoalveolar lavage fluid and in the lungs. these changes further lead to perivascular and peribronchiolar infiltration and inflammation. 31, 72 the formation of intra-alveolar foamy and haemosiderin-laden macrophages, smudge cells, alveolar damage, and hyaline membrane disease are seen in immunological and histopathological investigations. 67 it is known that hmpv infection induces toll-like receptor-dependent cellular signalling. however, the role of toll-like receptor-mediated signalling in the host's defence against pulmonary hmpv infection and pathogenesis is unknown. in a recent study, myd88-deficient mice were shown to have significantly reduced pulmonary inflammation and associated disease compared to wild-type c57bl/6 mice after intranasal infection with hmpv. 73 the molecular events in the pathogenesis of hmpv are shown in figure 4 . to date, there is no clear evidence to determine if hmpv remains limited to the respiratory tract during infection or if the virus can cause a systemic infection. there is some evidence that the latter is possible -one study showed the presence of hmpv in middle ear fluid 56 and another showed the presence of hmpv rna in the brain tissue of a patient who died of encephalitis, 74 but further investigation is needed. various cell lines, such as vero cells, 75 hep-2 cells, hep g2 cells, 76 293 cells, 29 and llc-mk2 cells 5 have been used for the growth and isolation of hmpv. in a recent study using 19 different cell lines to grow hmpv, it was shown that the most suitable cell lines for the growth of hmpv were a human chang conjunctiva cell line (clone 1-5c4) and a feline kidney crfk cell line. 77 in cell culture, hmpv has a slow growth rate, with late cytopathic effects varying from the rounding of cells and their detachment from the culture matrix to small syncytium formation. for this reason, the detection of hmpv antigen using anti-hmpv antibody in direct fluorescence or elisa-based assays is widely used along with cell culture methods. 75 the sensitivity and specificity of cell culture detection methods were found to be 68% and 99%, respectively, as compared to real-time rt-pcr detection of hmpv. 78 currently, the use of cell culture for the diagnosis of hmpv infection is uncommon and molecular methods like rt-pcr and/or real-time rt-pcr are more widely used. two studies have developed and evaluated multiplex pcr assays with the aim of providing a tool capable of detecting an increasingly complete panel of respiratory viruses. 79, 80 with the development of multiplex rt-pcr (mrt-pcr), it is now possible to design a more sensitive and rapid assay for the detection of hmpv. mrt-pcr methods have a sensitivity and specificity of 100% and 96%, respectively, compared to 54.6% and 100% for rrt-pcr. 81 another advantage of mrt-pcr is the ability to detect coinfections, even with very low viral loads that are undetectable via cell culture or immunostaining. 82 however, many clinical laboratories do not at present have the capability to perform routine diagnostic rt-pcr for hmpv detection. for rapid and accurate diagnosis of hmpv infections, a combination of immunofluorescence assays and direct fluorescent antibody methods is used as the first-line of diagnosis, followed by rt-pcr on the negative samples. 83 in the future, the availability of shell vial centrifugation culture and hmpv monoclonal antibodies will be of significant benefit for the rapid diagnosis of hmpv in clinical laboratories. currently, the treatments available for hmpv infection are primarily supportive. but a few reports have raised the possibility of using ribavirin, immunoglobulin, fusion inhibitors, and small interfering ribonucleic acids for the treatment and control of hmpv infection. [84] [85] [86] [87] [88] [89] [90] [91] the different strategies used to treat hmpv infection are reviewed in table 1 . several vaccine candidates against hmpv have undergone testing in rodent models and non-human primate models. although they have shown promising results, none has yet been tested in human volunteers. there may be problems -a heat inactivated viral vaccine against hmpv enhanced lung disease when tested in mice. 92 t cell epitope vaccines have been shown to reduce immunomodulation by hmpv challenge. murine animals immunized with an hmpv cytotoxic t lymphocyte epitope vaccine produced less th1 and th2 type cytokines compared to non-immunized mice following hmpv challenge. 93 a few studies have also evaluated immunization by chimeric vaccines against hmpv infection. when tested in hamsters and african green monkeys, chimeric vaccines for hmpv were shown to induce the production of neutralizing antibodies and confer immunity against a challenge with the wildtype. 94 a subunit vaccine, using the fusion protein of hmpv, has been shown to induce cross-protective immunity against hmpv challenge in the hamster. 95 several hmpv f subunit vaccines have given strong levels of protection when tested in rodents, hamsters, and non-human primates. [96] [97] [98] in a recent study, hmpv virus-like particles (vlps) mimicking the properties of the viral surface of both subgroups a and b were tested as a vaccine candidate. when tested in mice, these vlps were able to induce a strong humoral immune response against both heterologous and homologous strains. 99 although an hmpv-vlp vaccine seems to be a promising approach, more research is still warranted to develop a vaccine that will be effective against all of the subgroups of hmpv. the emergence of plasmid-based reverse genetics systems has given a significant boost to efforts to develop a live vaccine against hmpv infection. 100 recombinant hmpvs with sh, g, or m2-2 gene deletions have been evaluated for virus replication levels and it has been shown that the deletion of these genes does not affect the immunogenicity or the antigenicity of the virus. 18, 101 in a recent study, a live attenuated vaccine strain of hmpv was developed by changing the glycosylation site of the f protein. this vaccine was found to give complete protection against homologous virus challenge and some protection against heterologous viral challenge, even with a challenge at 56 days post-inoculation. 102 all these findings suggest that before an effective vaccine against hmpv can be developed, more detailed knowledge of the molecular pathogenesis of hmpv is required. human metapneumovirus is a relatively recently described virus 1 and hmpv appears to be as dangerous a pathogen as hrsv in terms of morbidity and mortality. as an important respiratory pathogen, understanding hmpv pathogenesis and molecular constraints for severe disease is essential for the treatment of infection and for the development of an effective vaccine against hmpv. recent studies using animal models for hmpv infection and reverse genetics platforms have shed some light on hmpv pathogenesis and have allowed us to evaluate live vaccine candidates. now we need to initiate the clinical trials to evaluate the 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against human metapneumovirus infection in mice the use of plasmid-based reverse genetics to generate influenza virus strains for improved vaccine production infection of nonhuman primates with recombinant human metapneumovirus lacking the sh, g, or m2-2 protein categorizes each as a nonessential accessory protein and identifies vaccine candidates a live attenuated human metapneumovirus vaccine strain provides complete protection against homologous viral infection and cross-protection against heterologous viral infection in balb/c mice the authors are grateful to dr nicole edworthy for her contribution towards the correction of the english language in the manuscript. the authors report no conflicts of interest and have not received any funds for this article. key: cord-257200-q0vqlerz authors: zumla, a.; mccloskey, b.; bin saeed, a.a.; dar, o.; al otabi, b.; perlmann, s.; gautret, p.; roy, n.; blumberg, l.; azhar, e.i.; barbeschi, m.; memish, z.; petersen, e. title: what is the experience from previous mass gathering events? lessons for zika virus and the olympics 2016 date: 2016-06-15 journal: int j infect dis doi: 10.1016/j.ijid.2016.06.010 sha: doc_id: 257200 cord_uid: q0vqlerz all previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis a, polio and meningitis. three mass gathering held in africa during the ebola outbreak accepted participants from west africa and was able to handle the theoretical risk without any incident. therefore we believe that the olympic games in rio de janeiro should not be cancelled. the number of visitors to the games is a tiny fraction (1%) of other visitors to zika endemic countries and it will have no measurable effect on the risk of spreading zika virus, if the games was cancelled. prediction is very difficult-especially about the future. thus we have to look at previous experience to allow an informed estimate to be made of the risk of holding the olympic games at the same time as an ongoing epidemic of a vector-borne viral infection. at the other end of the scale are unintentional 'mass gatherings' such as refugees taking shelter in huge camps, often in cramped conditions with poor hygiene. these are not usually regarded as mass gathering events, but nevertheless they pose the same problem in terms of the transmission of pathogens in the situation of a large number of people in a limited space. currently the civil war in syria has displaced many people, and diseases like tuberculosis, cutaneous leishmaniasis, measles, and polio are a risk. 1 such conditions also increase the risk of transmission of zoonoses, with expected closer contact to rodents compared to normal conditions. thus a one health approach is also needed in this situation. 2 mass gathering events are theoretically ideal situations for the spread of infections between people from very different and widespread geographical localities, with potentially different immune responses. one of the first events that focused the international health community on mass gathering events was the outbreak of meningitis in 2000-2001 after the hajj. 3, 4 however, the spread of infections is rarely caused by mass gathering sports events. 5 all previous experiences from different mass gathering show that vaccine preventable diseases is the most important infections like influenza, hepatitis a, polio and meningitis. three mass gathering held in africa during the ebola outbreak accepted participants from west africa and was able to handle the theoretical risk without any incident. therefore we believe that the olympic games in rio de janeiro should not be cancelled. the number of visitors to the games is a tiny fraction (1%) of other visitors to zika endemic countries and it will have no measurable effect on the risk of spreading zika virus, if the games was cancelled. the spread of severe acute respiratory syndrome coronavirus (sars-cov) from china to hong kong and further to canada was not due to a mass gathering, but to infected individuals travelling late in the incubation period or just after the onset of symptoms. 6, 7 the introduction of west nile virus to north america was probably through wild birds crossing the atlantic, and it could not have been predicted. lastly, the outbreak of middle east respiratory syndrome coronavirus (mers-cov) in korea was caused by a single traveller waiting in an overcrowded hospital emergency room in south korea. 8 the korean mers-cov outbreak illustrates how difficult it is to predict the future. mers was estimated to have a low epidemic potential, 9 and it was pointed out in this journal that the outbreak was identified as being caused by mers-cov because it happened in a country with the resources (knowledge and laboratory facilities) to rapidly identify the virus. 10 the sendai framework for disaster risk reduction (drr, 2015-203023) is the first of three united nations landmark agreements approved in 2015. the sendai framework has an emphasis on health and gives a clear mandate, emphasizing the need for more integrated drr that incorporates bottom-up as well as top-down approaches, local scientific and technical knowledge, and draws attention to synergies with other critical policy arenas including health, climate change, and sustainable development. over the next 15 years, the sendai framework has set out to achieve ''the substantial reduction of disaster risk and losses in lives, livelihoods and health and in the economic, physical, social, cultural and environmental assets of persons, businesses, communities and countries'' -including risk reduction at mass gatherings. 11 the use of science to inform decisions, an integral part of the sendai framework, must also be applied to mass gatherings. some infections like tuberculosis have a long incubation period of several years, and exposure at a mass gathering will not be apparent and may easily be overlooked. 12 the transmission of multidrug-resistant bacteria, for instance gram-negative bacteria hosted in the intestine, is another concern that has not been well studied. asymptomatic individuals are colonized with local bacteria and may be carriers for months. 13 september 4-19, 2015) shows that it was possible to handle the threat without cancelling the events. 14 the events all accepted participants from west africa. the hindu kumbh mela is a 3-month long religious conglomeration held every 3 years in four different cities of north india by rotation, the most famous being held in allahabad. this is considered to be the largest human gathering on earth. the last one held in allahabad in 2013 had 120 million visitors. kumbh mela does not involve a fixed human settlement, but the creation of temporary settlements of canvas, corrugated metal sheets, bamboo, nails, and rope in the flood plains of the rivers to house and feed millions of people for 3 months every 3 years. for kumbh mela people come by air, road, rail, and foot from within india, making it almost impossible to maintain detailed records of people movements. 15 the hajj, kingdom of saudi arabia the hajj brings approximately three million muslim pilgrims from all over the world to mecca every year. studies and reviews of surveillance data from returning pilgrims have shown that influenza, rhinovirus, and non-mers coronavirus are the most common pathogens, and suggest that influenza immunization before departure may be justified. [16] [17] [18] general screening for infections in pilgrims visiting the hajj has been reported in two other studies, 17, 19 which found influenza to be the most common respiratory pathogen. meningococcal disease is now rarely recorded. they also noted that gastroenteritis was common, but this is most probably due to lack of hygiene at the event. a study from australia looking at pre-travel prevention among pilgrims found that 80% were immunized against influenza, 30% against pneumococcus, and 30% against pertussis. concern about contracting disease at hajj was the most cited reason for vaccination (73.4%). those who obtained pre-travel advice were twice as likely to be vaccinated as those who did not seek advice. 20 since the 2000 and 2001 outbreak, bacterial meningitis has been a high priority for the kingdom of saudi arabia. several studies have looked at carrier rates of neisseria meningitidis in hajj pilgrims, and overall carriage rates of 5-10% were found, comparable to the rate found in populations in non-epidemic settings. 21 in 2000 and 2001, 338 and 316 cases of laboratoryverified neisseria meningitidis were reported; this fell dramatically to 2-4 cases per year (2013-2015) following the introduction of mandatory immunization with the quadrivalent vaccine. 22 the quadrivalent acwy polysaccharide meningococcal vaccine has been a visa requirement for hajj and umrah since 2002. at the same time the saudi authorities introduced a vaccination programme for children and adults living in mecca and medina, healthcare workers, and government personnel serving the pilgrims. 23 a recent study of bacterial infections and resistance to antibiotics in hospitalized hajj pilgrims in mecca found that escherichia coli was the most common bacterium (28%), followed by klebsiella pneumoniae and pseudomonas. methicillin-resistant staphylococcus aureus (mrsa) was found in 9.6%. 24 the potential spread of bacterial infections between hajj pilgrims -whether symptomatic or not -is also a concern because of the unrestricted prescription of antibiotics by local pharmacies to the pilgrims. 25 the most common outbreaks at mass gatherings, including religious mass gatherings other than hajj, sports events, and outdoor festivals, have involved vaccine-preventable infections, mainly measles and influenza, but also mumps and hepatitis a. 16 the psychology of individuals participating in mass gatherings the individual participant behaves in the context of their understanding of the norms associated with the group, and the relationships between group members become more trusting and supportive. understanding these two behavioural changes is key to understanding how and why mass gathering participants may behave in ways that make them more or less vulnerable to the transmission of infection. 26 vaccines are an important preventive tool for mass gatherings and should include the basic coverage provided by childhood immunization programmes, supplemented where appropriate with protection against meningitis and influenza, and yellow fever for mass gathering participants coming from yellow fever endemic countries. a review in this issue discusses the need for vaccines for mass gatherings and draws attention to immunization against pneumococcal infections in elderly pilgrims and highlights that polio may be a risk. 27 an important vaccine for hajj pilgrims, and the arabian peninsula in general, is one against mers-cov. the engineering of live attenuated vaccines has been facilitated by the development of reverse genetics. using one of these methodologies, viruses deleted in the small envelope (e) protein have been developed. these viruses have been attenuated and have induced protective humoral and cell-based immune responses in hamsters and mice after sars-cov challenge. 28 a meta-analysis on the use of face masks and the reduction in risk of upper respiratory infections found a modest effect. 29 compliance is always higher during a study than in the real-life situation, and making face masks mandatory at mass gatherings is not presently recommended. clearly there is a risk of zika virus (zkv) infection, but zkv is already present in more than 60 countries and the risk of spread already exists with or without the olympics. zikv spread from africa to southeast asia without any mass gathering event being involved, as far as we know, and its further spread to south america and between countries in south america has not been linked definitively to any mass gathering event. from the review of mass gathering experience in this special issue of the journal, vector-borne infections have not previously appeared as a particular risk, but experience also shows that potential health risks at a mass gathering can be mitigated effectively if they are recognized and planned for. the health authorities in brazil are aware of the vector-borne risks and have already managed several mass gatherings without evidence of significant international spread (e.g. annual rio carnival, world cup 2014). the estimated 500 000 visitors to the olympic games constitute less than 1% of visitors to the zkv endemic countries (and many of these travellers will come from countries already affected by zkv), so limiting travel to the olympics will not substantially affect the risk of zkv spread. 30 pregnant women should avoid visiting the olympics and those at risk of pregnancy should use contraception. for the individual non-pregnant traveller, zkv is a short febrile illness that leaves no sequelae. there is a small risk of complications like guillain-barré syndrome, but there is also a risk of ordinary influenza turning into severe double pneumonia requiring ventilator treatment, but we do not routinely immunize travellers to the tropics with year-round influenza transmission. travellers should be advised to follow standard precautions against insect bites, including applying repellent, wearing impregnated clothes, and using bed nets if they do not sleep in an airconditioned room. the available evidence does not support cancelling, postponing, or moving the 2016 olympic games and we hope that the games in rio de janeiro will be successful for the athletes and enjoyable for the public. conflict of interest: the authors declare no conflict of interest. communicable disease surveillance and control in the context of conflict and mass displacement in syria taking forward a 'one health' approach for turning the tide against the middle east respiratory syndrome coronavirus and other zoonotic pathogens with epidemic potential meningococcal disease and travel hajj-associated outbreak strain of neisseria meningitidis serogroup w135: estimates of the attack rate in a defined population and the risk of invasive disease developing in carriers public health. do sports events give microbes a chance to score? clinical features and short-term outcomes of 144 patients with sars in the greater toronto area a major outbreak of severe acute respiratory syndrome in hong kong probable transmission chains of middle east respiratory syndrome coronavirus and the multiple generations of secondary infection in south korea assessing the pandemic potential of mers-cov middle east respiratory syndromeadvancing the public health and research agenda on mers-lessons from the south korea outbreak reducing risks to health and wellbeing at mass gatherings: the role of the sendai framework for disaster risk reduction tuberculosis and mass gatherings-opportunities for defining burden, transmission risk, and the optimal surveillance, prevention, and control measures at the annual hajj pilgrimage prospective study of pathogens in asymptomatic travellers and those with diarrhoea: aetiological agents revisited hosting of mass gathering sporting events during the 2013-2016 ebola virus outbreak in west africa: experience from three african countries public health perspectives from the biggest human mass gathering on earth: kumbh mela, india communicable diseases as health risks at mass gatherings other than hajj: what is the evidence? infections in symptomatic travelers returning from the arabian peninsula to france: a retrospective cross-sectional study the spectrum of respiratory pathogens among returning hajj pilgrims: myth and reality active screening and surveillance in the united kingdom for middle east respiratory syndrome coronavirus in returning travellers and pilgrims from the middle east: a prospective descriptive study for the period 2013-2015 exploring barriers and facilitators of preventive measures against infectious diseases among australian hajj pilgrims: cross-sectional studies before and after hajj bin saeed aa. carriage of neisseria meningitidis in the hajj and umrah mass gatherings meningococcal disease during the hajj and umrah mass gatherings prevention of meningococcal disease during the hajj and umrah mass gatherings: past and current measures and future prospects antimicrobial resistance among pilgrims: a retrospective study from two emergency care hospitals mecca, saudi arabia community pharmacists' knowledge, attitude and practices towards dispensing antibiotics without prescription (dawp): a cross-sectional survey in makkah province, saudi arabia adding a psychological dimension to mass gatherings medicine hajj vaccinations-facts, challenges, and hope middle east respiratory syndrome vaccines uptake and effectiveness of facemask against respiratory infections at mass gatherings: a systematic review summer olympics key: cord-311413-uiwjrvru authors: chanda-kapata, pascalina; kapata, nathan; zumla, alimuddin title: covid-19 and malaria: a symptom screening challenge for malaria endemic countries date: 2020-04-27 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.007 sha: doc_id: 311413 cord_uid: uiwjrvru nan covid-19 and malaria: a symptom screening challenge for malaria endemic countries the unprecedented global coronavirus disease pandemic caused by sars-cov-2 has rapidly spread to all continents (who, 2020a) . whilst spread to africa has been slow, there are now increasing numbers of covid-19 being reported from african countries who are preparing themselves (kapata et al., 2020) for an exponential rise in numbers of cases. as of 24th march 2020, there have been 372,757 confirmed covidd-19 cases reported to the who with 16,231 deaths. in africa there have been 1305 cases with 25 deaths reported from 33 countries (who, 2020b) . in comparison, the who malaria report indicates that there were an estimated 228 million cases and 405,000 deaths due to malaria globally in 2018, majority of which were from the africa region (who, 2020c). covid-19 currently imposes an additional burden to the already overstretched, resource strapped health services which are grappling to bring under control the high burden of existing infectious and non-infectious diseases, including tb, hiv, and malaria. proactive screening for covid-19 is ongoing in high malaria endemic african countries. a case of covid-19 is deemed 'confirmed' based on a positive laboratory test result for sars-cov-2 virus infection regardless of symptoms (who, 2020b) . health care workers and community members alike are faced with an important challenge of quickly identifying symptoms and taking appropriate steps for laboratory investigation in line with the case definition based on surveillance or clinical characterisation (who, 2020a) . key steps to identifying a covid-19 case ultimately involves symptomatic or high risk patients presenting to health providers with complaints of any of the following symptoms or travel history: fever, cough, shortness of breath, fatigue, headache and others of acute onset or history of travel to affected areas or contact with an infected person. thus, current screening approaches for covid-19 are likely to miss approximately 50% of the infected cases even in countries with good health systems and available diagnostic capacities (gostic et al., 2020) . malaria shares some of the highly recognisable symptoms with covid-19 such as: fever, difficulty in breathing, fatigue and headaches of acute onset. thus, a malaria case may be misclassified as covid-19 if symptoms alone are used to define a case during this emergency period and vice versa. malaria symptoms appear within 10-15 days after an infective bite; multi-organ failure is common in severe cases among adults while respiratory distress is also expected in children with malaria, mimicking what is usually reported in patients with covid-19 (who, 2020c; white et al., 2014) . human travel history is also a significant consideration, like with covid-19, when screening for a suspected case of malaria as well as a means of curbing transmission (tatem and smith, 2010; chuquiyauri et al., 2012) . also, both covid-19 and malaria infected individuals may be asymptomatic for a long time while transmitting the infections through their respective modes (nishiura et al., 2020; chourasia et al., 2017) . globally, all countries are at very high risk of covid-19 while half of the world is at risk of malaria, with sub-saharan countries bearing the blunt of malaria cases and deaths while south east asia remain at high risk of both malaria and covid-19 (who, 2020b,c). although in sub-saharan africa the scale of the covid-19 outbreak is relatively lower than other regions, there are concerns that the situation may prove difficult with time considering the already weak health systems in the region (sambo and kirigia, 2014) . thus covid-19 and malaria converge symptomatically and geographically in most who regions. the definitive way to correctly identify the underlying infectious aetiology is through laboratory investigation and therefore availability of appropriate diagnostic capacity is essential for accurate surveillance and clinical management of cases. currently, it is expected that a high index of suspicion is skewed towards covid-19 given the alertness at community, health centre, country, regional and global level. in addition, another challenge is that people with fever may preferentially get tested for covid-19 and sent home due to a negative result and conversely febrile patients may get tested for malaria when they may in fact have covid-19 infection. the other case scenario is that patients may have malaria and covid-19 co-infection and diagnosis and treatment of one may lead to missing the other. a single case of covid-19 has the potential to transmit up to 3.58 susceptible individuals (chen et al., 2020a) . untreated malaria on the other hand has the potential to cause further community infections which in turn continues to be a significant source of illness and deaths globally (who, 2020c; challenger et al., 2019; chen et al., 2016) . thus undetected covid-19 virus and malaria parasite infections pose an immediate health challenge to the individual and public health consequences for the community (who, 2020b, c; challenger et al., 2019) . furthermore, there is concern that limited mobility and lockdowns, will interrupt the supply of malaria drugs. there is no specific treatment available for cvoid-19. hostdirected therapies including repurposed drugs such as antiretrovirals zinc, nutraceuticals, chloroquine, hydroxychloroquine are being considered (gautret et al., 2020; zumla et al., 2020) . what is required for africa is a low cost, safe, orally administered therapeutic which can reduce morbidity, mortality and duration of illness. the preliminary data on the use of chloroquine/azithromycin were encouraging (gautret et al., 2020) , although the trial was not randomised or controlled. conversely a small controlled study published from china showed no significant effect (chen et al., 2020b) . several large randomised trials are now underway and these will determine the usefulness of chloroquine for covid-19 treatment. countries are struggling to meet the testing demand for covid-19, while the malaria test kits are widely available at each point of care including the community level. there is need therefore for enhanced sensitisation on the potential of covid-19/malaria coinfections and further guidance to clinicians on the importance of testing for other causes of illness more so in this period when there is much emphasis to early detect and isolate covid-19 in a bid to contain further spread of the disease. since malaria tests are relatively more available (landier et al., 2016) , we recommend that health workers perform rapid tests for malaria as they screen for covid-19. this presents an opportunity to respond to two infectious diseases timely and reduce unnecessary morbidity and deaths. by rapidly ruling out malaria, the health workers can focus on the true cause of illness and administer appropriate management. the health and economic benefits/consequences in a real setting will provide valuable lessons for planners, clinicians, funders and governments on integrated management of infectious diseases. this issue is more relevant for travellers and people in malaria endemic countries as this is a season when malaria transmission is at its peak in sub-saharan africa (wang et al., 2020) . the global fund has already issued a guidance as of 4th march 2020 urging countries to 'reprogram savings from existing grants and to redeploy underutilized resources to mitigate the potential negative consequences of covid-19 on health and health systems' (the global fund, 2020). on an operational level, countries should look at how services for malaria and covid-19 are organised so as to efficiently use the available resources. for instance, malaria supplies could be moved to the laboratories or sites where the covid-19 testing is being done so as to reduce missed opportunities for malaria testing as some patients may be lost if they are declared covid-19 negative while in fact they may be malaria positive. the rollout of rapid malaria diagnostic tests (cunningham et al., 2019) , together with point of care tests for covid-19 (nguyen et al., 2020) when they are rolled out should be a priority. the reorganisation of services at health facility level has been a useful approach in tb/hiv collaborative activities (burnett et al., 2018) . there is a possibility that lymphopenia seen in patients with covid-19 may increase vulnerability to malaria, tb and other infections. as the world commemorates world malaria day on 25th april, 2020 in the midst of the covid-19 pandemic, the challenge still remains on how to ensure the progress made in malaria control is not setback. none declared. effect of tb/hiv integration on tb and hiv indicators in rural ugandan health facilities how delayed and non-adherent treatment contribute to onward transmission of malaria: a modelling study asymptomatic" malaria: a chronic and debilitating infection that should be treated a mathematical model for simulating the phase-based transmissibility of a novel coronavirus a pilot study of hydroxychloroquine in treatment of patients with common coronavirus disease-19 (covid-19) additional burden of asymptomatic and sub-patent malaria infections during low transmission season in forested tribal villages in chhattisgarh, india sociodemographics and the development of malaria elimination strategies in the low transmission setting a review of the who malaria rapid diagnostic test product testing programme hydroxychloroquine and azithromycin as a treatment of covid-19: results of an open-label non-randomized clinical trial estimated effectiveness of symptom and risk screening to prevent the spread of covid-19 is africa prepared for tackling the covid-19 (sars-cov-2) epidemic, lessons from past outbreaks, ongoing pan-african public health efforts, and implications for the future the role of early detection and treatment in malaria elimination the rate of underascertainment of novel coronavirus (2019-ncov) infection: estimation using japanese passengers data on evacuation flights 2019 novel coronavirus disease (covid-19): paving the road for rapid detection and point-of-care diagnostics. micromachines (basel) 2020 investing in health systems for universal health coverage in africa international population movements and regional plasmodium falciparum malaria elimination strategies the global fund preparedness is essential for malaria-endemic regions during the covid-19 pandemic public health round-up who corona virus situation report no 64 who: malaria factsheet. 2020 available from host-directed therapies and holistic care for tuberculosis all authors have a specialist interest in emerging and reemerging pathogens. dr. nathan kapata and sir prof. alimuddin zumla are members of the pan-african network on emerging and re-emerging infections (pandora-id-nethttps://www.pandora-id.net/) funded by the european and developing countries clinical trials partnership the eu horizon 2020 framework programme for research and innovation. sir zumla is in receipt of a national institutes of health research senior investigator award. key: cord-261672-0cresfn8 authors: kim, sungchan; jeong, yong dam; byun, jong hyuk; cho, giphil; park, anna; jung, jae hun; roh, yunil; choi, sooyoun; muhammad, ibrahim malik; jung, il hyo title: evaluation of covid-19 epidemic outbreak caused by temporal contact-increase in south korea date: 2020-05-14 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.036 sha: doc_id: 261672 cord_uid: 0cresfn8 objectives: on march 15, 2020, 61.3% of the confirmed cases of covid-19 infection are associated with the worship service that was organized on february 9 in the shincheonji church of jesus in daegu, south korea. in this study, we aim to evaluate the effects of mass infection in south korea and assess the preventive control intervention. method: using opened data of daily cumulative confirmed cases and deaths, the basic and effective reproduction numbers was estimated using a modified susceptible–exposed–infected–recovered-type epidemic model. results: the basic reproduction number was estimated to be [formula: see text]. the effective reproduction number increased approximately 20 times after the mass infections from the 31 st patient, which was confirmed on february 9 in the shincheonji church of jesus, daegu. however, the effective reproduction number decreased to less than unity after february 28 owing to the implementation of high-level preventive control interventions in south korea, coupled with voluntary prevention actions by citizens. conclusion: preventive action and control intervention were fairly established in south korea. in december 2019, people in wuhan, china began to contract pneumonia, and the cause was unknown. the condition was similar to viral pneumonia, as confirmed by clinical presentation. on january 7, 2020, it was confirmed that the cause of the pneumonia was a new coronavirus. thereafter, this was named the 2019 novel coronavirus disease-covid-19. notably, covid-19 induces mild symptoms that are similar to those induced by other respiratory infections. however, particularly, it affects older people with comorbidity and can result in fatal respiratory diseases (chen et al. 2020 ). on january 10, 2020, the chinese authorities reported the first death due to covid-19. after that, cases have been reported in other countries such as thailand and japan. in south korea, the first patient who had a history of visiting wuhan, was reported on january 20, 2020. since then, confirmed cases of covid-19 have been reported, and 30 patients were reported until in daegu and that she attended the church service on february 9 and 16 after she had experienced the symptoms of covid-19 on february 7. in addition, it was revealed that 5,006 confirmed cases, which accounted for 61.3% of the 8,162 confirmed cases, were associated with the church cluster in daegu (korean ministry of health and welfare 2020). accordingly, kcdc guessed that on february 9, the mass infections had occurred, resulting in many secondary cases, and so covid-19 rapidly propagated in south korea. as covid-19 rapidly spread nationwide from february 18, koreans have actively worn masks since then. furthermore, the government of korea recognized the seriousness of the spread of covid-19 and accordingly elevated the covid-19 alert from level 3 to 4 (the highest level) on february 23. the government has implemented the social-distancing campaign, enhanced the infection prevention and control practices in hospitals, conducted drive-through testing, and postponed the schedule of school activities. it is still committed to preventing the occurrence of covid-19. in this study, we establish a mathematical model using the early data of confirmed cases that were reported from january 20 to march 15 in korea. on the basis of the epidemiological investigation, the spreading process of covid-19 during this period is divided into three phases. in addition, we estimate the reproduction number of each phase to analyze the transmission potential and severity of covid-19. consequently, we assess the current situation of covid-19 in korea. we use a modified susceptible-exposed-infected-recovered transmission model to evaluate the covid-19 epidemic in korea. susceptible individuals enter the exposed class 1 after the transmission of the virus. we consider the linear chains , = 1,2, ⋯ , on the exposed class for determining a model that can be fitted to the data with limited information that the mean incubation period is 1/ , fixed (martcheva 2015; champredon et al. 2018 ). the exposed people were infected and entered the class. the terms and denote isolated and discharged, respectively. the term ( ) denotes the transmission rate. the parameters 1/ and 1/ denote the average duration from onset of symptoms to isolated, and average duration from isolated to discharged, respectively. the parameter is the case fatality rate. we have the following: to represent the temporal changes of contact, we consider the time-dependent transmission rate, ( ). we assume the initial transmission rate to be constant, i.e., ( ) = 0 before = 1 . after = 1 , we assume that the transmission rate rapidly increases as ( ) = 1 . after = 2 , upon introducing a high level of preventive control campaigns, the transmission rate is assumed to exponentially decay at the rate (althaus 2014) . we have the following: notably, the above-mentioned exponential decay implies that the change rate of , ′( ) is proportional to − ( ) with rate . we introduce the following two key measurements that describe the infection spread: the basic reproduction number 0 and the effective reproduction number (jones 2007) . the term 0 denotes the number of secondary infections generated by an infected case in wholly susceptible circumstances, and denotes the number of secondary infections generated in the current state of the population while implementing control interventions. a reproduction number higher than unity means continued disease transmission. however, the value lower than unity means that the continuous transmission has ended, and the disease gradually decreases and disappears. particularly, the basic reproduction number 0 in our model is simply given as follows: and the effective reproduction number, , is given as follows: the total population size was assumed to be 50,000,000. we regard as a constant because the number of deaths is small, relative to the total population size. we used the method of least squares to estimate the model parameters to minimize the following sum of squared residual until the sampling time : where data ( ) and data ( ) are cumulative data of the number of isolated and death at the th sampling time, respectively. we used the daily cumulative cases and deaths data that were publicly available from the kcdc. we level to the highest so that the preventive action was strictly implemented. therefore, we assume that 1 = 18 and 2 = 27(days). we made some assumptions to reduce the number of our estimated parameters for fitting the data. first, the incubation period was fixed to 1/ = 5.1(days) as the average incubation-period estimate of the covid-19 outbreak in wuhan, china (lauer et al. 2020) . it was reported 66 fatal cases as of march 12, 2020, and the time taken from experiencing symptoms to confirming is about 4.5 days and the time taken from test to confirming is about 0.5 days (jeong et al. 2020 ). so, we used 1/ = 3(days) while assuming the presumed self-isolation to be approximately one day. the period from being isolated to discharged was taken to be 14.7 days from the data reported until march 13, 2020 from kcdc (korean ministry of health and welfare 2020). so, we used 1/ = 14.7 + 1.5 = 16.2(days) that was collaborated with our assumption. transmission rate 0 , 1 , case fatality rate , and decay rate were estimated. we considered 100-chain model. = 100 was obtained as a result of fitting with the condition 1/ = 5.1. in this study, we aimed to evaluate the effects of mass infection due to temporal increases in contacts and assess the preventive control interventions using the confirmed cases and deaths data associated with covid-19 in korea. the first patient was reported on january 20, 2020, but the transmission of the infection actually started from the 3rd confirmed patients from january 22 in korea. since then, the covid-19 outbreak in korea has resulted in 29 confirmed cases by february 18. in addition, it appeared that the outbreak was going to be controlled. it was shown that 0 = 1.77 in our model analysis. this is slightly lower than that of wuhan, china ( 0 = 2.24~3.58) (zhao et al. 2020) . personal hygiene, such as wearing masks, handwashing and disinfecting items, seemed to have been maintained a certain level, thus far, the covid-19 outbreak is ongoing in many countries. for example, as of march 23, 2020, countries such as italy, the united states, spain, germany, and france still have more than 3,000 confirmed cases per day and more than 100 deaths per day. however, in korea, the outbreak has been reduced, as confirmed by the value of to less than unity within 10 days after the first mass infection was noticed. accordingly, we suggest that the government policy of "social distancing" which had been implemented in korea until april 5 and extended to may 5 may be maintained even at a lower level. covid-19: cases in singapore estimating the reproduction number of ebola virus (ebov) during the 2014 outbreak in west africa equivalence of the erlang-distributed seir epidemic model and the renewal equation epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study coronavirus disease-19: the first 7,755 cases in the republic of korea notes on r0 a mathematical model for assessing the effectiveness of controlling relapse in plasmodium vivax malaria endemic in the republic of korea korean ministry of health and welfare. coronavirus disease-19, republic of korea the incubation period of coronavirus disease 2019 (covid-19) from publicly reported confirmed cases: estimation and application an introduction to mathematical epidemiology transmission potential and severity of covid-19 in south korea preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak key: cord-266253-oyid5haj authors: al-abaidani, i.s.; al-maani, a.s.; al-kindi, h.s.; al-jardani, a.k.; abdel-hady, d.m.; zayed, b.e.; al-harthy, k.s.; al-shaqsi, k.h.; al-abri, s.s. title: overview of preparedness and response for middle east respiratory syndrome coronavirus (mers-cov) in oman date: 2014-10-29 journal: int j infect dis doi: 10.1016/j.ijid.2014.10.003 sha: doc_id: 266253 cord_uid: oyid5haj several countries in the middle east and around 22 countries worldwide have reported cases of human infection with the middle east respiratory syndrome coronavirus (mers-cov). the exceptionally high fatality rate resulting from mers-cov infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. within the framework of the national acute respiratory illness surveillance, the ministry of health in the sultanate of oman has announced two confirmed cases of mers-cov to date. the aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. the absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in oman. several countries worldwide have reported cases of human infection with the middle east respiratory syndrome coronavirus (mers-cov). the exceptionally high fatality rate resulting from mers-cov infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. 1 the ministry of health in the sultanate of oman has announced two confirmed cases of mers-cov. the aim of this report is to describe the epidemiological aspects of the reported mers-cov cases in oman and to highlight the public health response and the activities done to face any future resurgence of mers-cov in the country. based on the world health organization (who) interim case definition for mers-cov as of july 3, 2013, 2 the first laboratory-confirmed case of mers-cov in oman was diagnosed on october 29, 2013. a 68-year-old omani man from dakhliyah governorate complained of fever and cough of 2-day duration. he then developed right lower lobe pneumonia and multi-organ failure and died on november 10, 2013. he had a history of type 2 diabetes mellitus and uncontrolled hypertension, and he had previously undergone coronary artery bypass grafting. he did not have a history of travel outside the country or contact with animals. the second case was a 59-year-old omani man from north batinah governorate who presented on december 22, 2013 with a high-grade temperature and cough of 6-day duration. he later developed severe right upper lobe pneumonia and died on december 30, 2013. he was a heavy smoker, but had no known medical comorbidities. the patient had attended a camel race in abu dhabi, uae, 4 weeks before the onset of his symptoms. the ministry of health implemented a national mers-cov preparedness and response plan. this plan was based on the exceptionally high fatality rate resulting from mers-cov infection in conjunction with the paucity of knowledge about this emerging virus has led to major public and international concern. within the framework of the national acute respiratory illness surveillance, the ministry of health in the sultanate of oman has announced two confirmed cases of mers-cov to date. the aim of this report is to describe the epidemiological aspects of these two cases and to highlight the importance of public health preparedness and response. the absence of secondary cases among contacts of the reported cases can be seen as evidence of the effectiveness of infection prevention and control precautions as an important pillar of the national preparedness and response plan applied in the health care institutions in oman. strengthening five pillars of action, including public health surveillance and contact management, building laboratory capacity, infection prevention and control, case management, and risk communication. algorithms were developed describing response actions in the event of a suspected mers-cov case. checklists for the preparedness of health care facilities were developed and action plans were later developed to rectify the deficiencies. field visits were conducted immediately after confirmation of cases by the regional and national rapid response teams from the ministry of health, and contact surveillance and monitoring was conducted for 14 days after the last exposure. laboratory surveillance for mers-cov started by building laboratory diagnostic capacity with the availability of the primers for mers-cov testing, and with the training of laboratory personnel countrywide on the triple-packing and shipment of samples. training on how to collect nasopharyngeal swabs for testing for mers-cov was conducted for emergency room physicians, internists, and intensivists in all district hospitals. national infection prevention and control guidelines were developed for dealing with suspected or confirmed cases of mers-cov. mask-fit testing was done for all healthcare workers who could be involved in taking care of patients with mers-cov. a project was initiated for triaging of patients presenting to emergency rooms or health centers with an acute respiratory illness. in 2013, post hajj surveillance for mers-cov was done using nasopharyngeal swabs for people returning from hajj and presenting with respiratory symptoms. three hundred and fifty samples were tested by real-time pcr and all were negative for mers-cov. the surveillance system for severe acute respiratory infections (sari) was implemented in oman in january 2008 in four regional hospitals as sentinel sites; sari aims to determine the epidemiology of severe respiratory infections and the contribution of influenza and other etiological agents to severe respiratory infections in the country. 3 it also aims to detect emergent influenza strains with pandemic potential or any other respiratory infections, and to detect any unusual morbidity or mortality due to acute respiratory illness. in 2012, sari sentinel sites were used as a platform to test 10% of cases for mers-cov at the central public health laboratory; 2000 samples were tested and all were negative. in conclusion, we have described the epidemiological aspects of the two reported cases of mers-cov in oman and the preparedness efforts made by the ministry of health. strengthened infection control practices and having a powerful active surveillance program for acute respiratory illnesses is key to the rapid and prompt response for emerging respiratory infections. conflict of interest: none. middle east respiratory syndrome coronavirus (mers-cov): summary and literature update revised interim case definition for reporting to who-middle east respiratory syndrome coronavirus (mers-cov) world health organization. interim global epidemiological surveillance standards for influenza key: cord-275866-m89hgf41 authors: li, ping; chen, lulu; liu, zheming; pan, jinghui; zhou, dingyi; wang, hui; gong, hongyun; fu, zhenmin; song, qibin; min, qian; ruan, shasha; xu, tangpeng; cheng, fan; li, xiangpan title: clinical features and short-term outcomes of elderly patients with covid-19 date: 2020-05-31 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.107 sha: doc_id: 275866 cord_uid: m89hgf41 abstract background the outbreak of coronavirus disease 2019 (covid-19) has become a global public health emergency. methods 204 elderly patients (≥60 years old) diagnosed with covid-19 in renmin hospital of wuhan university from january 31st to february 20th, 2020 were included in this study. clinical endpoint was in-hospital death. results of the 204 patients, hypertension, diabetes, cardiovascular disease, and chronic obstructive pulmonary disease (copd) were the most common coexisting conditions. 76 patients died in the hospital. multivariate analysis showed that dyspnea (hazards ratio (hr) 2.2, 95% confidence interval (ci) 1.414 to 3.517;p < 0.001), older age (hr 1.1, 95% ci 1.070 to 1.123; p < 0.001), neutrophilia (hr 4.4, 95% ci 1.310 to 15.061; p = 0.017) and elevated ultrasensitive cardiac troponin i (hr 3.9, 95% ci 1.471 to 10.433; p = 0.006) were independently associated with death. conclusion although so far the overall mortality of covid-19 is relatively low, the mortality of elderly patients is much higher. early diagnosis and supportive care are of great importance for the elderly patients of covid-19. the severity of symptoms variable was categorized as mild, severe, or critical. mild cases included non-pneumonia and mild pneumonia cases. severe was characterized by dyspnea, respiratory frequency ≥ 30/minute, blood oxygen saturation ≤ 93%, pao2/fio2 ratio <300, and/or lung infiltrates >50% within 24-48 hours. critical cases were those that exhibited respiratory failure, septic shock, and/or multiple organ dysfunction/failure 8 . medians and interquartile ranges were calculated as summaries of continuous variables. for categorical variables, percentages of patients in each category were determined. poor outcome was defined as the earliest of death. the time to death were investigated using survival analysis with follow up starting at hospital admission and ending on 20 february 2020. the primary end point was death. patients were censored if at the end of the end of follow up they were still alive (for mortality). the kaplan-meier method was used for time-to-death plot. comparisons between groups of time-to-death data were made using the cox proportional hazards model. a multivariate cox proportional hazards model was used to analyze independent risk factors for mortality from the three variables: age, onset of dyspnea, presence of any comorbidities. the same method was used to identify risk factors for adverse outcomes. spss (version 22.0) was used for all statistical analyses. a p value of less than 0.05 is considered statistically significant. the initial study cohort comprised of 209 elder patients. five patients who contracted j o u r n a l p r e -p r o o f 5 covid-19 while in the hospital during a prolonged stay that began well before the the median time between the onset of symptoms and admission was 10 days (7-14 days). the iqr time from self-reported earliest known exposure to onset of symptoms was 11days (7-15days) for prodrome (fatigue or myalgia), 10 days (7-14 days) for selfreported fever, 11 days (8-14 days) for diarrhea, and 10 days (7-14 days) for cough or dyspnea. laboratory data on admission are shown in table 2 the univariate cox proportional hazards model showed that the mortality risk was 5.3 times of that in those aged above 70 (95% confidence interval (ci) 3.1 to 9.0; p<0.001). for every 5 years increase in age, the risk of death increased by 1.55. however, there was no difference in the proportion of men and women with mortality. the initial state of covid-19 at admission is closely associated with mortality in the elderly. severe or critical cases were associated with an increased mortality risk of 10 (95% ci 5.4 to 14.6; p<0.001).the presence of any comorbidities increased the mortality risk (hazards ratio (hr) 3.1, 95% ci 1.6 to 5.8; p=0.001), with copd (hr 3.1, 95%ci 1.8 to 5.4 ; p< 0.001) and chronic renal failure (hr 4.2, 95% ci 1.7 to 10.5; p=0.002), being the most important comorbidities ( table 2 ). the presence of cardiovascular disease with an increased mortality of 1.8 (95% ci 1.1 to 2.9; p=0.016), similar to hypertension with an increased mortality of 2.3 (95% ci 1.5 to 3.6; p<0.001)(figure 2).other j o u r n a l p r e -p r o o f 8 comorbidities factors (cancer and diabetes mellitus) had no significant effects on mortality. in addition, onset of dyspnea before admission increased the mortality risk (hr 2.0, 95% ci 1.3 to 3.2; p=0.002). leucocytosis, neutrophilia, ph values, ckmb levels, , ultra-tni, d-dimer, albumin, procalcitonin, partial pressure of carbon dioxide, the partial pressure of oxygen, and oxygen saturation were also associated with death ( we conducted a cohort of 204 elder patients over 60 years who were hospitalized with covid-19 in wuhan, china. we observed similar clinical features as recently reported covid-19. the most common symptoms were fever, cough, and dyspnea. fever was the first symptom reported by many patients (78.9%). the onset of dyspnea might help physicians identify the patients with poor prognosis.35.3% patients were classified as severe or even critical cases on admission. the overall rate of serious illness was higher than those reported in previous studies. in addition, a significant portion of patients showed bilateral infiltrate chest radiograph results on admission. univariate analysis showed age of 70 years or older, comorbidity (hypertension, j o u r n a l p r e -p r o o f cardiovascular disease, copd, chronic renal failure), onset of dyspnea, and several laboratory indices abnormalities were associated with poor outcome. in our multivariable cox proportional hazards model, dyspnea, older age, neutrophilia and elevated ultra-tni were independently associated with poor outcomes. in this study, we reported 76 death of covid-19. most patients had pulmonary consolidation and hypoxemia which was difficult to recover. the clinical characteristics of these patients indicated that the age and underlying diseases were the most important risk factors for death. for every 5 years increase in age, the risk of death increased by 1.55. the most common underlying disease was hypertension, followed by cardiovascular disease, diabetes, copd, malignant tumors, and kidney disease. the effects of age and comorbidities have also been addressed in other cohorts of patients with covid-19 4,5 . the presence of cancer or diabetes mellitus was related to a higher mortality rate or an adverse outcome in other studies 4 , which could predispose to superimposed nosocomial pneumonia due to staphylococcus aureus or other agents in these already critically ill patients, although this was not observed in our patients. however, the presence of copd, chronic renal failure, cardiovascular disease or hypertension was related to a higher mortality rate in our data. the patients with underlying disease of lung, heart, and kidney are more vulnerable to severe acute respiratory syndrome coronavirus 2 (sars-cov-2), most likely because angiotensin converting enzyme ii (ace2) protein has an abundant expression in many kinds of cells, such as renal tubular epithelial cells, alveolar epithelial cells, heart, artery smooth muscle cells 9 . the coronavirus has a three-dimensional structure of spike j o u r n a l p r e -p r o o f protein, which is closely bound to human cell receptor ace2. therefore, the cells with ace2 expression may act as target cells and be susceptible to covid-19 infection, such as type ii alveolar cells (at2) in the lung 10 . in terms of laboratory tests, the count of lymphocytes in most patients was reduced. this result suggests that covid-19 is a viral disease characterized by decreased lymphocyte count, like those recently reported 4, 5, 11 . although lymphopenia has been commonly observed, the absolute lymphocyte count was not associated with poor outcome in our study. most patients' albumin levels and 84.8% hemoglobin levels were decreased, which indicates that malnutrition is common to elderly patients. elevated alanine aminotransferase and aspartate aminotransferase levels were prevalent on admission in our cohort. high levels of d-dimer was found in more than half of patients with infection. these findings are quite different from those associated with pneumonia caused by common bacterial pathogens, but similar to those previously observed in patients with sars-cov infection 12, 13 . the routine blood test and pct were used to reflect changes in the inflammatory response in covid-19. increased white blood cell and neutrophils count were observed in 30.64% and 33.33% of patients. in particular, a high neutrophil count was an independent predictor for poor outcome. neutrophilia was observed during the cytokine storm induced by virus infection [14] [15] [16] . in the study of betsy et al, after autopsy they showed neutrophils infiltrating lung in the context of a cytokine storm triggered ards and caused organ damage and mortality in covid-which will seriously damage the lung function and resulted in dyspnea and acute respiratory failure when fluid builds up in the air sacs in lungs. elevated levels of ultra-tni was more commonly seen in covid-19. cardiac complications were common in patients with pneumonia in our cohort. the high level of ultra-tni was another independent predictor for poor outcome. the present understanding of the human cardiovascular response to infections, including pneumonia, is derived mainly from studies of critically ill patients with septic shock 17 . further research is needed to investigate the pathogenesis of sepsis in covid-19 illness. in the largest case series to date of covid-19, a total of 1,023 deaths have occurred among 44,672 confirmed cases for an overall case fatality rate of 2.3% 3 , and the ≥80 age group had the highest case fatality rate of all age groups at 14.8%. however, in our case series,≥ 60 years old age group had a case fatality rate of 37.3% which is much higher. the possible explanation is that the cases in our cohort are from the stage of the epidemic outbreak. most of the patients have to be isolated at home without medical support due to a lack of inpatient beds in the hospital. two-third of patients in our studies had received empirical therapy out of hospital over ten days before their admission with covid-19. so that their illness was from mild to severe. moreover, the case fatality rate of is unsurprisingly highest among critical cases at 75%. however, it is difficult to calculate the true mortality rate of the disease while the epidemic is continuing and it is impossible to ascertain which of the remaining patients will eventually die or be discharged. until now, no specific antiviral treatment has been recommended for coronavirus j o u r n a l p r e -p r o o f infection. once infected, the older patients are harder to treat without supportive care. currently, the approaches to control this disease is to prevent the sources; use of personal protective equipment to reduce the transmission; and early diagnosis, isolation, and supportive treatments. this study suggests that the elderly patients of covid-19 have a rapid course of the disease and a higher case fatality ratio. severe cases on admission were often subjected to higher death rates. according to current diagnostic criteria, viral nucleic acid test results confirmed by rt-pcr assay play a vital role in determining whether to hospitalize a patient. the overall sensitivity of the rt-pcr test for coronavirus in patients was only 59% 18 which needs to be improved. this might be affected by sample quality, the methods of obtaining the samples, as well as the viral load. early diagnosis and supportive care in the hospital are of great importance for the elderly covid-19 patients. the elderly patient with acute dyspnea should seek medical attention immediately. the results of this study must be interpreted with caution and this research is subject to several limitations. this was a retrospective case series study based on data from medical records. clinical notes and patient charts. accordingly, certain information was missing for various patients, and certain data that may have been based on patient memory, such as details concerning exposure history and timing of onset of symptoms, maybe affected by recall bias. not all laboratory tests were done in all patients. laboratory parameter is not all documented in our studies. finally, in an effort to quickly disseminate information to clinicians worldwide, we only assessed short-term outcomes. the follow-up evaluation to determine the long-term repercussions of this world health organization. novel coronavirus(2019-ncov): situation report 51 characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of cases from the chinese center for disease control and prevention clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical features of patients infected with 2019 novel coronavirus in wuhan clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interimguidance the novel coronavirus pneumonia emergency response epidemiology t. the (covid-19) -china tissue distribution of ace2 protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis a pneumonia outbreak associated with a new coronavirus of probable bat origin clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan a major outbreak of severe acute respiratory syndrome in hong kong preliminary clinical description of severe acute respiratory syndrome new fronts emerge in the influenza cytokine storm on the alert for cytokine storm: immunopathology in covid-19 targeting potential drivers of covid-19: neutrophil extracellular traps acute pneumonia and the cardiovascular system correlation of chest ct and rt-pcr testing in monocyte count abbreviations: iqr, interquartile range; inr, international normalized ratio; ckmb, creatine kinase-mb; ultra-tni, ultrasensitive cardiac troponin i; ph, pondus hydrogenii; pco 2 , partial pressure of carbon dioxide abbreviations: copd, chronic obstructive pulmonary disease 95% ci, 95% confidence interval; ckmb, creatine kinase-mb; ultra-tni, ultrasensitive cardiac troponin i; ph, pondus hydrogenii key: cord-274845-pqvlh3eg authors: li, yan; wang, jiangshan; wang, chunting; yang, qiwen; xu, yingchun; xu, jun; li, yi; yu, xuezhong; zhu, huadong; liu, jihai title: characteristics of respiratory virus infection during the outbreak of 2019 novel coronavirus in beijing date: 2020-05-07 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.008 sha: doc_id: 274845 cord_uid: pqvlh3eg abstract background coronavirus disease 2019 (covid-19) is spreading. here, we summarized the composition of pathogens in fever clinic patients and analyzed characteristics of different respiratory virus infection. methods retrospectively collected patients with definite etiological results using nasal and pharyngeal swabs in fever clinic. results totally, 1860 patients were screened and 136 patients were enrolled. 72 (52.94%) of them were diagnosed as influenza (flu) a virus infection. 32 (23.53%) of them were diagnosed as flu b virus infection. 18 (13.24%) and 14 (10.29%) of them were diagnosed as covid-19 and respiratory syncytial virus (rsv) infection respectively. covid-19 group had a higher rate of contact with epidemic area within 14 days and clustering onset than other groups. fever was the most common symptom in these patients. the ratio of fever and the highest temperature were higher in flu a virus infection patients than in covid-19 patients. covid-19 patients had lower white blood cell count and neutrophil count than flu a virus and rsv infection group, but higher lymphocyte count than flu a and b virus infection groups. covid-19 group (83.33%) had higher rate of pneumonia in chest ct scan than flu a and b virus infection groups. conclusions influenza viruses accounted for a large proportion of respiratory virus infection even during the epidemic of covid-19 in beijing. no single symptom or laboratory finding was suggestive of specific respiratory virus, however, epidemic history was important for screening of covid-19. which is spreading in china [1] , and influenza a h1n1, the severe acute respiratory syndrome coronavirus (sars-cov) and the middle east respiratory syndrome coronavirus (mers-cov) that emerged in the past decade [2] [3] [4] . 2019-ncov is payed much attention recently [5] , and disease caused by 2019-ncov was named as covid-19, short for "coronavirus disease 2019", by world health organization [6] . however, other respiratory viruses, even though not that widely spreading, can also cause similar symptoms as 2019-ncov does and should not be ignored. here, we summarized the composition of pathogens in fever clinic patients and analyzed characteristics of different respiratory viruse infection. patients with fever (oral temperature >=37.3℃) or respiratory symptoms (cough, sputum, pharyngalgia, rhinorrhea, dyspnea and so on) were suggested to go to fever clinics for screening in beijing. peking union medical college hospital (pumch) had a fever clinic for screening. also, to strictly control the development of the epidemic situation of covid-19, all patients with epidemiologic history of covid-19 (there was a history of travel or residence in wuhan and its surrounding areas and communities with reported cases within two weeks before the onset of the disease; or within 14 days before the onset of the disease, contacted with covid-19 j o u r n a l p r e -p r o o f 5 patients (with positive nucleic acid test); or within 14 days before the onset of the disease, contacted with patients with fever and respiratory symptoms from wuhan and its surrounding areas and communities with reported cases; or there was clustering onset of disease) [7] were required to screen even though without fever or respiratory symptoms at pumch. clustering onset was defined as two or more cases of fever and / or respiratory symptoms were found in a small area such as family, office, school class and other places within two weeks. patient's medical records were taken by doctors containing the symptoms, signs, epidemic history and so on. epidemic history contained: 1) contacted with epidemic area within two weeks before the onset of the disease; 2) contacted with confirmed or suspected cases within two weeks before the onset of the disease; 3) contacted with poultry, livestock or wild animals (especially dead animals) within two weeks before the onset of the disease; 4) clustering onset. nasal and pharyngeal swabs were collected by clinicians with statistical analysis was finished by spss statistics 17.0. the normality of the distribution was assessed using the kolmogorov-smirnov test. group t-test was applied to the normal distribution data and mann-whitney u test was applied to the non-normal distribution data. data are shown as means±sd or median(25%-75%). chi square test was used for comparison of two or multiple rates or components. analyses were presented as two-sided comparisons. the p value less than 0.05 was considered to be significant. fever was the most common symptom in the respiratory virus infection patients. all the patients of flu a virus infection had fever, the ratio was higher than that in there was no statistical difference in complete blood count parameters between similar to what was reported in covid-19 [9] , fever was the most common symptom in the respiratory virus infection patients. in this study, the ratio of fever and the highest temperature were higher in flu a virus infection patients than in covid-19 patients. given to the absence of fever and low grade fever in covid-19 patients and its high risk [10, 11] , it was feasible to ask fever free patients with respiratory symptoms to screen as it was previously recommended [11] . even though the rate of pharyngalgia, headache, myalgia and fatigue were relatively higher in influenza infection groups, it could not be said that presence of these symptoms was page 10 of 18 j o u r n a l p r e -p r o o f 10 meaningful for excluding covid-19 because they were not specific symptoms in different respiratory virus infection. indeed, no specific symptoms were helpful in distinguishing covid-19 from other respiratory virus infection [11] . as it was previously reported, covid-19 patients had low or normal wbc and neutrophil count [9, 10] . and in this study, it showed that covid-19 patients even had lower wbc count and neutrophil count than flu a virus and rsv infection group. also, it was reported that they had low lymphocyte count [9, 10] , but this study found that the lymphocyte count was higher in covid-19 than in flu a and b virus infection patients. this results said that low wbc, neutrophil and lymphocyte were suggestive of viral infection, but could not distinguish different respiratory virus. also, even though crp level was higher in rsv infection group than in covid-19 and flu b infection group, but it was not statistically different in flu a infection, flu b infection and covid-19 groups. however, it was possible that lower wbc and lymphocyte levels and higher crp level might be more valuable in monitoring the disease severity rather than in screening for covid-19 [10] . the value of cbc parameters and crp deserved more study in respiratory virus infection. the percentage of pneumonia in chest ct scan was higher in covid-19 group than in flu a and b virus infection group. it was in accordance with other studies that showed covid-19 patients were likely to had pneumonia [9, 10] . and covid-19 should be vigilant if it showed pneumonia in chest ct scan during the spreading of 2019-ncov, as what was recommended in a screening procedure in fever clinic [11] . and chest ct scan might be a fast and convenient tool in the distinguishing ground-glass opacity a novel coronavirus emerging in china -key questions for impact assessment critically ill patients with 2009 influenza a(h1n1) in mexico epidemiological, demographic, and clinical characteristics of 47 cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study a major outbreak of severe acute respiratory syndrome in hong kong c2/files/b218cfeb1bc54639af227f922bf6b817.pdf characteristics and outcome of viral pneumonia caused by influenza and middle east respiratory syndrome-coronavirus infections: a 4-year experience from a tertiary care center clinical features of patients infected with 2019 novel coronavirus in wuhan clinical characteristics of 2019 novel coronavirus infection in china clinical features of 2019 novel coronavirus infection patients and a feasible screening procedure none. key: cord-262310-z0m6uuzf authors: effenberger, maria; kronbichler, andreas; shin, jae il; mayer, gert; tilg, herbert; perco, paul title: association of the covid-19 pandemic with internet search volumes: a google trendstm analysis date: 2020-04-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.033 sha: doc_id: 262310 cord_uid: z0m6uuzf abstract objectives to assess the association of public interest in coronavirus infections with the actual number of infected cases for selected countries across the globe. methods we performed a google trendstm search for “coronavirus” and compared relative search volumes (rsv) indices to the number of reported covid-19 cases by the european center for disease control (ecdc) using time-lag correlation analysis. results worldwide public interest in coronavirus reached its first peak end of january when numbers of newly infected patients started to increase exponentially in china. the worldwide google trendstm index reached its peak on the 12th of march 2020 at a time when numbers of infected patients started to increase in europe and covid-19 was declared a pandemic. at this time the general interest in china but also the republic of korea has already been significantly decreased as compared to end of january. correlations between rsv indices and number of new covid-19 cases were observed across all investigated countries with highest correlations observed with a time lag of -11.5 days, i.e. highest interest in coronavirus observed 11.5 days before the peak of newly infected cases. this pattern was very consistent across european countries but also holds true for the us. in brazil and australia, highest correlations were observed with a time lag of -7 days. in egypt the highest correlation is given with a time lag of 0, potentially indicating that in this country, numbers of newly infected patients will increase exponentially within the course of april. conclusions public interest indicated by rsv indices can help to monitor the progression of an outbreak such as the current covid-19 pandemic. public interest is on average highest 11.5 days before the peak of newly infected cases. a novel coronavirus, the acute respiratory syndrome coronavirus 2 (sars-cov-2), causes a new disease named corona virus disease 2019 . it was first detected in december 2019 in wuhan (hubei, china) (wang et al., 2020) . due to a high virulence and a high proportion of asymptomatic cases, the outbreak spreads all over the world. on april 5 th 2020 the world health organization (who) reported 1 133 758 confirmed cases. today, a cumulative mortality rate of 5.5 % (62 784) has been reported. the internet is increasingly used as a source of health care information. infodemiology and infoveillance are essential public health informatics methods which are used to analyze search behavior on the internet. infodemiology is defined as "science of distribution and determinants of information in an electronic medium, specifically the internet, or in a population, with the ultimate aim to inform public health and public policy", while the primary aim of infoveillance is surveillance (eysenbach, 2009) . infodemiology and infoveillance of epidemiological data are important to increase situational awareness and make suitable interventions (rivers et al., 2019) . the analysis of relative internet search volumes (rsv) gives information on the extent of public attention (arora et al., 2019 , kaleem et al., 2019 , ling and lee, 2016 with google trends tm being one of the most widely used tools for this purpose. rsv are used for real-time analyses for transmissibility, severity, and natural history of an emerging pathogen, as observed with severe acute respiratory syndrome (sars), the 2009 influenza pandemic, and ebola (chowell et al., 2009 , cleaton et al., 2016 . the analyses of confirmed cases are particularly useful to infer key page 5 of 18 j o u r n a l p r e -p r o o f 5 epidemiological parameters, such as the incubation and infectious periods and ongoing outbreaks or an outbreak probability. in addition, google trends tm data might be used to forecast an increase in infected cases. a linear time series pattern with official dengue reports, indicating a potential use to monitor public interest before an increase of cases and during the outbreak (husnayain et al., 2019) . beside infectious diseases, google trends tm have been successfully used to forecast the suicide risk increase (barros et al., 2019) . in this study, we investigated the public interest in covid-19 since december 31 st 2019 comparing google trends™ data to data of newly infected covid-19 cases. retrieving outbreak and confirmed cases numbers from the who data on confirmed covid-19 cases were retrieved on the 5 th of march from the european center for disease control (ecdc) for the time from the 31 st of december 2019 until the 1 st of april 2020 (https://www.ecdc.europa.eu/en/publicationsdata/download-todays-data-geographic-distribution-covid-19-cases-worldwide). worldwide data were retrieved as well as data for the following countries, namely china, republic of korea, japan, iran, italy, austria, germany, the united kingdom (uk), the united states (us), egypt, australia, and brazil. retrieving google trends tm data on covid-19 the google trends tm tool was used to retrieve data on internet user search activities in the context of covid-19. google trends tm enables researchers to study trends and patterns of google tm search queries (arora et al., 2019) . it was implemented in j o u r n a l p r e -p r o o f 6 trends tm expresses the absolute number of searches relative to the total number of searches over the defined period of interest (arora et al., 2019) . the retrieved google trends tm index ranges from 0 to 100, with 100 being the highest relative search term activity for the specified search query in the time period of interest. further information on google trends tm can be found on the respective help page worldwide interest in coronavirus started on january 20 th and reached its first peak on january 31 st , a few days after the word was spread on the outbreak in wuhan, china. the increasing numbers of cases over the globe prompted the who to declare the coronavirus outbreak as a pandemic on march 11 th , leading to an increase in public interest currently peaking on march 12 th 2020 ( figure 1 ). the data on newly confirmed cases, overall confirmed cases, and overall death worldwide as 7 well as for the afore-mentioned countries under study are summarized in table 1. there are two peaks, one sharp increase in numbers when cases were counted based on clinical diagnosis and not from a confirmatory laboratory test in china and the other peak on march 16 th due to cases around the globe. the worldwide initial peak associates with a strong increase of confirmed cases in china. in china, a maximum of google trends tm rsv was observed at the end of january with a 5.47-fold increase of cases between january 24 th and january 28 th . afterwards, with rigorous measures the relative increase in new cases was slower, and a decrease of new cases was firstly reported to the who on february the 6 th , with the exception of a sharp increase as mentioned above. the rsv trend followed a similar path, with a steady number of search enquiries around 25% of the maximal interest during the last weeks. (figure 2 ). correlation analysis indicates highest public interest in covid-19 on average around 11.5 days before the maximum of newly infected cases was reported ( figure 3 ). in countries with proximity to china such as the republic of korea or japan a high volume of search queries was observed during or closely after the peak was reached in china. a non-comparable smaller peak was observed in countries in the european union or the us (figure 2 ). in the republic of korea, a first google trends™ index peak was observed end of january only slightly shifted as compared to the peak in china with a second peak being observed on february 23 rd (figure 2 ). this second peak in korea proceeded the peak in newly infected cases by 7 days (figure 3 ). japan´s rsv started to increase on february 24 th , with a peak on february 27 th , also followed by an increase in confirmed covid-19 cases. in iran, the most affected country in the middle east, a strong increase of rsv could be observed on february 18 th with a peak between 20 th and 22 nd of february. the iranian increase of rsv was five days page 8 of 18 j o u r n a l p r e -p r o o f 8 before the first confirmed cases in iran, with also a strong association and prediction of the outbreak, which followed five to seven days later. egypt, the first country on the african continent with a confirmed covid-19 case, showed a small rsv peak during the outbreak in china. furthermore, the rsv started to steadily increase since february 20 th with an observed leap in interest on april 1 st . australia showed a similar pattern with an increase in rsv during the first outbreak in china, followed by a decrease afterwards and again an increase since february 23 rd , followed by increasing new covid-19 cases 10 days later (figure 2 ). in european countries, especially in italy, a small peak in the google trends tm analysis was found during the outbreak in china and a climax was found on february 23 rd 2020, a few days before the numbers of newly covid-19 started to increase exponentially. similar trends were observed in austria, germany and the uk with a delay of several days and a second peak, which was accompanied by an increase in numbers in the following days. the highest rsv peak was reached mid of march , which is in line with rigorous policies by the government regarding the rapid spread. the uk and australia show very similar patterns with highest correlations between rsv indices and newly diagnosed cases found with time lags of -12 and -7 days respectively ( figure 3 ). in the us, a steady increase of google tm search queries since february 27 th was observed followed by an outbreak since march 2 nd . the peak of search queries was march 3 rd a new increase in rsv is found in brazil, followed by increasing numbers of newly confirmed cases of covid-19 ( figure 2 ). in our study, we found a significant increase in rsv using google trends™ for covid-19 worldwide with a peak of rsvs around 11.5 days prior to the peak in newly diagnosed cases in different countries all over the world. as such, google trends™ can be used to associate and predict outbreaks worldwide and provides a valuable picture of the outbreak of covid-19 in real time. close monitoring and continued evolution of enhanced communication strategies is needed that provide general populations and vulnerable populations most at risk with actionable information for self-protection, including identification of symptoms (heymann et al., 2020) . the application of internet data in health care research, also known as infodemiology, is a promising new field and it may complement and extend the current data sources and foundations (mavragani and ochoa, 2019) . the attention to covid-19 increased days to weeks before the actual peak outbreak, not only worldwide, but also in most of the investigated countries in this study. this strongly supports our finding that the rsv is a useful tool to monitor local and global outbreaks of infectious diseases. the internet is the biggest platform for search engines and social media for real time data and outbreaks. rsv has been used before to detect outbreaks, like the recent severe influenza outbreak in 2009 (cook et al., 2011) . close monitoring and continued evolution of enhanced communication strategies is needed that provide general populations and vulnerable populations most at risk with actionable page 10 of 18 j o u r n a l p r e -p r o o f 10 information for self-protection, including identification of symptoms (heymann et al., 2020) . most countries and the who provide awareness -raising and educational programs on covid-19 via internet. the strong association between rsv and increasing outbreak numbers may be due to implementation of such programs in the different countries. the impact of web based research continuously grows since the past decade (jun et al., 2018) . google trends™ is the only unbiased approach including millions of users and has widely been used in health issues. public attention in different fields has been published recently (e.g. osteoarthritis, breast cancer or copd) (boehm et al., 2019 , jellison et al., 2018 , kaleem et al., 2019 . furthermore, infodemiology and google trends™ is used to generate awareness profiles and is a suitable substitute for classical data collection, such as surveys (jun et al., 2018) . far mostly, google trends™ is used to monitor disease control and awareness in cancer, hiv or stroke, but also in rare diseases like antiphospholipid syndrome or systemic lupus erythematosus (ling and lee, 2016 , mahroum et al., 2019 , sciascia and radin, 2017 , sciascia et al., 2018 . definitely, google trends™ can be used to detect success rates of awareness programs and predict infectious outbreaks worldwide (mclean et al., 2019 , patel et al., 2020 . there are also some potential limitations of this study. there is no information about the individual searches for the analyzed topics. the selections of spelling/terms might affect the results and conclusions. the importance of accuracy in defining the search queries is exemplified by searching google trends™ for the topic "pneumonia". pneumonia is associated with covid-19, although not specifically representing covid-19. thus, using the query "pneumonia" may be useful to analyze symptom-related curiosity, but does not sufficiently represent covid-19 outbreaks. the number of studies based on google trends™ is increasing, but so far there is no standardized procedure for data collection. more guidance by google™ should be warranted in order to assist researchers to establish an optimal search strategy (nuti et al., 2014) . despite the fact the google search is accessible worldwide, the use of different search tools in certain countries like for example baidu in china might lead to more accurate estimations of public interest. it was for example shown that a high baido search index (bsi) predicted dengue fever outbreaks in guangzhou and to a lesser degree in zhongshan, indicating that bsi might complement traditional dengue fever surveillance in china (liu et al., 2016) . in our study we decided to make use of data from one common framework. in conclusion, infodemiology and rsv provide a tool to anticipate covid-19 outbreaks and of other infectious diseases. information on public interst could be used to monitor the outbreak in northern european countries, africa or the americas. cases, with highest interest observed on average 11.5 days before the peak of newly reported covid-19 cases google trends: opportunities and limitations in health and health policy research the validity of google trends search volumes for behavioral forecasting of national suicide rates in ireland using google trends to investigate global copd awareness severe respiratory disease concurrent with the circulation of h1n1 influenza characterizing ebola transmission patterns based on internet news reports assessing google flu trends performance in the united states during the 2009 influenza virus a (h1n1) pandemic infodemiology and infoveillance: framework for an emerging set of public health informatics methods to analyze search, communication and publication behavior on the internet technical advisory group for infectious h. covid-19: what is next for public health? correlation between google trends on dengue fever and national surveillance report in indonesia using google trends to assess global public interest in osteoarthritis ten years of research change using google trends: from the perspective of big data utilizations and applications google search trends in oncology and the impact of celebrity cancer awareness disease monitoring and health campaign evaluation using google search activities for hiv and aids, stroke, colorectal cancer, and marijuana use in canada: a retrospective observational study using baidu search index to predict dengue outbreak in china capturing public interest toward new tools for controlling human immunodeficiency virus (hiv) infection exploiting data from google trends google trends in infodemiology and infoveillance: methodology framework internet search query analysis can be used to demonstrate the rapidly increasing public awareness of palliative care in the usa the use of google trends in health care research: a systematic review success of prostate and testicular cancer awareness campaigns compared to breast cancer awareness month according to internet search volumes: a google trends analysis using "outbreak science" to strengthen the use of models during epidemics what can google and wikipedia can tell us about a disease? big data trends analysis in systemic lupus erythematosus infodemiology of antiphospholipid syndrome: merging informatics and epidemiology the authors declare no conflicts of interest. not applicable key: cord-305788-z75yv88e authors: agergaard, charlotte nielsen; lis-tønder, joanna; olsen, dorte aalund; kierkegaard, helene; møller, jens kjølseth title: challenging diagnostics in familial transmission from asymptomatic covid-19 carrier. should we group sars-cov-2 samples from households? date: 2020-09-28 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1442 sha: doc_id: 305788 cord_uid: z75yv88e nan dear editor in chief, by march 8, 85 covid-19 cases had been diagnosed in denmark and mid-march an estimated 50% of imported cases derived from austria [https://files.ssi.dk/covid19-overvaagningsrapport-12032020, correa-martínez et al., 2020] . march 3 to 8 a 49-year-old, man went skiing in ischgl, austria accompanied by 11 male friends. few days after returning to denmark, six travel companions developed symptoms of covid-19 and were tested sars-cov-2 pcr positive. according to the danish guidelines at that time, none of the six asymptomatic individuals was tested. however, one of these, the 49-year-old man and his family of four arranged a self-imposed two-week home quarantine on march 11. approximately one week later his wife and 18-year-old daughter developed influenza-like symptoms. the following week the 15-year-old daughter developed ageusia while the 8-year-old old daughter presented her usual recurrent cough. extension of the national covid-19 testing april 1 led the family to the local test-center, where the indexperson and the daughter presenting ageusia tested sars-cov-2 pcr positive. the wife and two other daughters tested negative. the three negative specimens together with 197 sars-cov-2 negative samples from other patients were retested at an external laboratory. all samples remained negative; but the specimens from the wife and youngest daughter were found weakly positive. their initial pcr curves were reassessed and found equally irregular with ct-values of 32 and 35. three weeks later, all five displayed a serologic sars-cov-2 n/s igg response. the asymptomatic indexperson and the youngest daughter presenting the highest igg-titers (chemiluminescence immunoassay (clia), iflash1800 shenzhen yhlo). comparative testing with the sars-cov-2 s1/s2 igg assay (clia, diasorin, liaison) found the index-person and three daughters positive and the wife just below cut-off (table 1) . this family cluster incorporates several aspects of the challenges surrounding covid-19 and sars-cov-2 diagnostics. the familial transmission from an asymptomatic carrier who displayed a positive sars-cov-2 pcr four weeks after infestation and a subsequent immunologic response. the wife and three daughters, who j o u r n a l p r e -p r o o f had mild symptoms of covid-19, presented diverse and divergent sars-cov-2 pcr results, yet displayed an immunologic response. this family case implies the importance of duration of infectiousness from an asymptomatic carrier [chan et al., 2020 , huang et al., 2020 . secondly, that symptoms and generation of specific antibodies varies even among closely related family members, supporting the potential benefit of sars-cov-2 detection from a combination of nucleic acid testing and time-related serology [fafi-kremer et al., 2020 , flodgren 2020 , okba et al., 2020 . finally, that covid-19 diagnostics and containment measures might benefit from grouping samples from households in order to collectively assess results and potential need of repeat sampling [winichakoon et al., 2020] . oral and written informed consent to describe this family cluster was obtained from the father on behalf of the family. a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster a pandemic in times of global tourism: super spreading and exportation of covid-19 cases from a ski area in austria serologic responses to sars-cov-2 infection among hospital staff with mild disease in eastern france immunity after sars-cov-2 infection, 1st update -a rapid review 2020 ssi. covid-19 in denmark, an epidemiological surveillance report a family cluster of sars-cov-2 infection involving 11 patients in nanjing, china severe acute respiratory syndrome coronavirus 2−specific antibody responses in coronavirus disease 2019 patients negative nasopharyngeal and oropharyngeal swabs do not rule out covid-19 the authors declare that there are no conflicts of interests. this research did not receive any specific grant from funding agencies in the public, commercial, or not-forprofit sectors. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.j o u r n a l p r e -p r o o f key: cord-276254-q04hqra2 authors: paul, kishor kumar; salje, henrik; rahman, muhammad w.; rahman, mahmudur; gurley, emily s. title: comparing insights from clinic-based versus community-based outbreak investigations: a case study of chikungunya in bangladesh date: 2020-06-02 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.111 sha: doc_id: 276254 cord_uid: q04hqra2 abstract background outbreak investigations typically focus their efforts on identifying cases that present at healthcare facilities. however, these cases rarely represent all cases in the wider community. in this context, community-based investigations may provide additional insight into key risk factors for infection, however, the benefits of these more laborious data collection strategies remains unclear. methods we used different subsets of the data from a comprehensive outbreak investigation to compare the inferences we make in alternative investigation strategies. results the outbreak investigation team interviewed 1,933 individuals from 460 homes. 364 (18%) of individuals had symptoms consistent with chikungunya. a theoretical clinic-based study would have identified 26% of the cases. adding in community-based cases provided an overall estimate of the attack rate in the community. comparison with controls from the same household revealed that those with at least secondary education had a reduced risk. finally, enrolling residents from households across the community allowed us to characterize spatial heterogeneity of risk and identify the type of clothing usually worn and travel history as risk factors. this also revealed that household-level use of mosquito control was not associated with infection. conclusions these findings highlight that while clinic-based studies may be easier to conduct, they only provide limited insight into the burden and risk factors for disease. enrolling people who escaped from infection, both in the household and in the community allows a step change in our understanding of the spread of a pathogen and maximizes opportunities for control. infectious disease outbreaks have the potential to place a significant burden on public health resources. understanding who is at risk of becoming infected is critical for the focused targeting of interventions. due to relative ease of access and limited cost requirements, outbreak investigations typically focus on cases that present at formal healthcare centers such as hospitals or community clinics. for example, data collection performed as part of epidemiological investigations during the recent epidemics of ebola, zika and mers focused on quantifying the number of cases and their characteristics. (al-abdallat et al., 2014 , lu et al., 2015 , teixeira et al., 2016 these case-counting exercises provided key insights into fundamental epidemiological parameters such as the basic reproductive number and case fatality rates, and allowed the projection of the future course of the epidemic. (aylward et al., 2014 , lessler et al., 2014 , lewnard et al., 2014 , yamin et al., 2015 however, without information on the underlying population, and especially characteristics of individuals who avoid infection, these approaches limit our ability to make mechanistic insights, quantify burden of disease, and identify risk factors for infection, hampering efforts to develop targeted control strategies. cases that present at healthcare centers may only represent a small minority of all cases. in addition, some individuals are more likely to visit formal healthcare providers than others, including those with more severe illness, and differences in healthcare seeking can vary by age, gender and socioeconomic status. (chowdhury et al., 2007 , nikolay et al., 2017 , pandey et al., 2002 household-based outbreak investigations, where investigation teams visit affected j o u r n a l p r e -p r o o f communities, permit a more comprehensive understanding of pathogen spread that limits the impact of healthcare seeking patterns. (france et al., 2010) however, these investigations are usually still focused on identifying individuals that got sick. (boore et al., 2013 , france et al., 2010 without also understanding who is avoiding infection in a community, it is difficult to identify the key risk factors for infection, limiting potential inferences. the possible insights from alternative investigation strategies have not previously been systematically compared. here, we use the results of a detailed chikungunya outbreak investigation from bangladesh as an example to consider the inferences made under different investigation scenarios. chikungunya virus is a mosquito-borne alphavirus transmitted to humans by aedes mosquitoes causing acute fever, joint pain, and skin rash. (aubry et al., 2015) chikungunya fever was first recognized in 1952 in tanzania. (lumsden, 1955) since then, outbreaks of chikungunya have been regularly identified across the tropics and sub-tropics. the first chikungunya outbreak in bangladesh was identified in 2008 in two northwestern districts bordering india.(icddr) since then regular outbreaks have been detected. (khatun et al., 2015 , salje et al., 2016b here we use the results from a detailed investigation of an outbreak of chikungunya virus in a village in tangail, bangladesh where the outbreak team visited every household in the community and interviewed all members in each household. the comprehensive household investigation captured both those who did get infected and those that escaped from infection. the objective of this study was to compare our approach, in terms of the inferences about the outbreak, to more limited investigation strategies. in late november 2012, a local health official of gopalpur sub-district in tangail households in the village consented to being enrolled in the study. questionnaires were administered in all households to identify suspected cases, identify demographic characteristics, and travel histories of individuals within households. suspect cases were defined as residents with acute onset of fever with rash or joint pain within 6 months prior to beginning the investigation. study staff administered questionnaires to household heads about household members' demographic data and history of illness, water source, construction materials, and mosquito control measures in the household. potential mosquito breeding containers in and around the participating households with stored water were inspected for presence of larvae. suspected cases were asked about their symptoms with onset date and specifics about their treatment seeking behavior. the gps location of all homes was also recorded. determining the etiology of the outbreak all household members, irrespective of their suspected case status, were asked to provide a single 5 ml blood specimen for laboratory testing. blood specimens were spun in the field to separate serum, which were then stored on ice and transported to the virology laboratory of iedcr. the serum samples were tested for igm antibodies against chikungunya by enzyme linked immunosorbant assay (elisa) (standard diagnostics, inc., south korea). suspected casepatients who had igm antibodies against chikungunya in their serum were termed laboratory confirmed cases. we created four different datasets that allowed us to consider different outbreak investigation strategies: this dataset consisted of all suspect cases that reported that they visited a formal healthcare setting (defined as government or non-government primary healthcare center/clinic/hospital) following the onset of symptoms. this dataset consisted of all suspect cases, irrespective of their healthcare seeking behaviors. this dataset consisted of all suspect cases plus controls consisting of household members of these cases. this dataset consisted of all members of all households in the community, regardless of symptoms. the epidemic curve was constructed using symptom onset date of chikungunya cases. gps locations of households with and without chikungunya cases were used to prepare spatial distribution maps. for the case-only datasets (datasets a and b), we compared the age and sex distribution of the cases with that for the district from the 2011 census (bangladesh bureau of statistics, 2011) . for the datasets with information on individuals who escaped from infection (datasets c and d), we initially used simple logistic regression to compare the demographics, typical apparel worn, travel history within the last six months, and household characteristics of cases with non-cases. we then built multivariable logistic regression models to identify adjusted risk factors for chikungunya fever. we initially placed all variables with a p-value of <0.05 in the unadjusted analysis into a multivariable model. we then used backward stepwise selection using the akaike information criterion (aic) (sauerbrei et al., 2007) to identify the best model. not all individuals who get infected will present with symptoms. we attempted to capture these individuals by asking for blood samples from all community members. to assess the impact of j o u r n a l p r e -p r o o f misclassifying asymptomatically infected individuals as controls in datasets c and d, we conducted sensitivity analyses where these individuals were reclassified as cases. all participants provided written informed consent prior to interviews and blood specimen collection and the ministry of health and family welfare, government of bangladesh reviewed and approved the outbreak investigation plan. the ninety-five suspect cases reported visiting a formal healthcare facility for symptoms consistent with chikungunya between july and november, with the peak number of cases occurring in j o u r n a l p r e -p r o o f october (figure 1 : panel a). cases sought care in three different centers: 25 sought care in a government run community clinic, 8 in a government run sub-district health complex and 62 in a private clinic. the median age was 28 years (interquartile range (iqr) = 14-45 years) and the majority (60%) were female (table 1 ). if we used the age and sex distribution of the district from the 2011 national census, we find that there is an increased risk of disease in those between the ages of 30-49 compared to those aged below 10 years (or 2.51, 95% 1.24-5.51) and that females were at increased risk of infection compared to males (or of 1.43, 95% ci: 0.94-2.23) ( table 2) . an additional 269 suspect cases were identified in the community who did not seek care in formal healthcare facilities. of these, 246 individuals visited a local pharmacy and 21 individuals visited the informal sector (unlicensed medical practitioner, traditional healer, and homeopath). the distribution of dates of symptom onset for all cases was nearly identical to the distribution for those that visited clinics (spearman correlation of 0.95) ( figure 1a ). the proportion of suspect cases visiting a clinic varied between 18% in 51-55 years age group and 44% in ≤5 years age group ( figure 1b) . the conclusions about age, sex, educational levels, use of mosquito controls and clinical presentation of suspect cases were similar when using datasets of all cases or only those that sought care in clinics (table 1) , however, those who presented to clinics were more likely to travel outside the district (41% vs 28%, p-value 0.001). cases who attended formal healthcare settings also appeared to come from similar parts of the community as cases who did not (figure 2a-b) . similar to the analysis using clinical cases only, using data from the national census identified increasing risk among females for being a case (table 2) . inference from community cases plus controls from same household j o u r n a l p r e -p r o o f incorporating controls from the households where cases reside allowed us to assess additional potential risk factors for being a case. consistent with inferences using census data, logistic regression models that used household controls also identified increased risk among females (aor 1.75, 95% ci 1.31-2.36) ( table 2 ). in addition, this analysis showed that cases were significantly less likely to have secondary (aor 0.64, 95% ci 0.42-0.98) or more formal (higher secondary) education (aor 0.28, 95% ci 0.17-0.47) compared to the household controls. incorporating data from the entire community showed that the chikungunya outbreak was largely constrained to the center of the village, with few households affected on the east and west borders but virtually all households affected in the center ( figure 2c ). this is despite the entire community only being a few hundred meters wide. the expanded dataset also allowed us to understand the risk factors for infection in the wider community. as with the previous analyses, females had an increased risk of being a case (or: 1.62, 95% ci 1.29-2.03) ( table 2 ), although the difference by sex was concentrated in adults with no difference among children ( figure 1c ). further individuals who reported usually wearing clothing that exposed both limbs had 1.80 the odds of being a case compared to individuals wearing clothing that exposed upper limbs only (95% ci 1.30-2.50). those who had travelled outside tangail district within the last six months also had increased odds of being a case (aor 1.47, 95% ci 1.06-2.03). individuals who had higher secondary or more formal education (aor 0.38, 95% ci 0.24-0.62) were less likely to be a case than individuals without formal education. we did not identify any household characteristics that were associated with being a case, including presence of mosquito larvae (aor 0.87, 95% ci: 0.66-1.16), daily use of anti-mosquito coil (aor 1.03, 95% ci: 0.82-1.31), number of j o u r n a l p r e -p r o o f household members (aor 1.00, 95% ci: 0.79-1.26), and number of rooms in the household (aor 1.11, 95% ci: 0.82-1.51). fifty-two individuals without symptoms tested positive for chikv. we found no significant demographic differences between symptomatic suspected cases and igm-confirmed asymptomatic cases in those who gave blood (table s1 ). in sensitivity analysis, we removed these individuals from the 'control' population and included them in the 'case' populations. risk factors for being a case identified in the previous analysis remained similar in both scenarios where we considered household contacts as controls and individuals from all community households as controls (supplementary information, table s4 ). however, we found important differences in the probability of providing blood. those with symptoms were 6.1 times more likely to provide blood than those without symptoms. further, among asymptomatic individuals, only 2% of children 0-9 years provided a sample compared to 15% among those 30-49 (table s2 ). there were also significant differences by sex (14% of asymptomatic males gave blood compared to 8% of females, p-value <0.001) and educational level with more educated people less likely to provide samples (table s2 ). outbreak investigations are central to informed responses to public health emergencies caused by the emergence of an infectious pathogen. however, outbreak investigations currently largely revolve around case-counting exercises that limit our ability to identify who is at risk for j o u r n a l p r e -p r o o f infection and who is not. here, by using the results of a comprehensive outbreak investigation, we have been able to explicitly explore the impact of different investigation strategies in the same outbreak. we found that a clinic-based study that used data from all the formal healthcare settings would have identified a quarter of all cases and, using census data, have correctly identified female sex as an important risk factor for disease. however, it is only through the recruitment of people who did not get sick that we could identify the importance of travel history, educational level and apparel usage in determining who gets sick. controls from the wider community were also required to demonstrate which household-level characteristics were important for risk, showing that the use of mosquito coils was not protective, and to map spatial heterogeneity in risk, key to intervention development and deployment. this study highlights the significant heterogeneity in healthcare seeking. even in a small community such as this, cases visited nine different sources of healthcare, three of which could be considered formal healthcare settings. infectious disease surveillance activities are unlikely to be able to collate datasets from this diverse range of healthcare sources, even among only those within formal sector, suggesting that outbreak investigations that rely on cases that seek healthcare likely substantially underestimate the magnitude of outbreaks. using the results of our study, we provide our assessment of the ability of different investigation strategies to capture key characteristics of an outbreak (table 3 ). in practice, the decision to expand outbreak investigations beyond information available from healthcare systems will depend on the resources available. where outbreak teams are already performing communitybased case-investigations, the additional time and effort to also collect data on those without symptomsboth from case-households as well as neighboring householdsmay be marginal. this comprehensive outbreak investigation employed ten field-based investigators and took seven days to complete. an investigation strategy only focused on cases in the community would have taken only marginally less person-time as finding cases in the community anyway typically requires comprehensive door-to-door surveys. our findings highlight how this additional data collection effort can help reveal the drivers of transmission, allowing mechanistic insight into pathogen spread and maximizing opportunities to control, many of which would not be possible from case-based investigations (table 3 )..where it is collected, an additional major benefit of the comprehensive dataset is that it can inform mathematical models that reconstruct entire outbreaks, allowing us to estimate the mean transmission distance (previously estimated here at 95 meters) (salje et al., 2016b) . travelling outside tangail district within the six months before the outbreak was associated with increased chikungunya fever risk. human movement can introduce chikv into new areas, causing epidemics (chretien and linthicum, 2007) . no other areas of bangladesh were reporting outbreaks of chikv at this time, though outbreaks may have been missed due to poor surveillance. although individuals of all ages were affected by chikungunya in this outbreak, incidence increased with age among females, potentially linked to increased time women spend at home compared to males, increasing their risk of being bitten by the largely home-dwelling aedes mosquito (salje et al., 2016b) . in this outbreak, household use of mosquito coils was not protective against chikungunya, which is consistent with the findings from a recent meta-analysis on household level risk factors for dengue, which is also spread through aedes mosquitoes (bowman et al., 2016) . serum samples have the potential to provide important information about the level of asymptomatic infection during an outbreak, as has previously been shown during previous chikv outbreaks (salje et al., 2016a , sissoko et al., 2008 . in addition, this outbreak investigation was carried out six months after the outbreak began and community members may have been unable to reliably recall their symptoms or the date their symptoms started, particularly for milder illnesses, which may have led to an underestimation of suspected cases. serological confirmation could help detect any missing infections. however, our study highlights how some caution needs to be taken when interpreting serological data. firstly, while we sought to obtain blood samples from all participants, only one in five individuals agreed. we found that the probability of agreeing to provide blood depended strongly on having had chikungunya symptoms (individuals who had symptoms were more likely to provide samples). children, women and those with a high educational level were less likely to give blood. secondly, the sensitivity of the commercial assay we used has been estimated to be <40% in individuals where igm is still circulating (johnson et al., 2016) and is likely to be even lower here, as the blood draw occurred after igm antibodies would have waned to undetectable levels for many infected individuals (kam et al., 2012) . future studies should consider underlying biases in who is providing blood as well as considering the use of complementary igg assays to help improve the interpretability of serological findings. this investigation suggests that chikungunya virus has become an emerging public health problem in bangladesh, and outbreak investigations of emerging infections often have the objective of estimating attack rates of diseases and identifying the risk factors that lead to infection. our analysis suggests that the optimal strategy for attaining these objectives during an outbreak is to conduct case finding, testing, and data collection in communities. many recent j o u r n a l p r e -p r o o f outbreaks of emerging infections have suffered due to a lack of detailed information about attack rates and risk for infection, due to their limited investigation strategies (ahmed et al., 2015 , ballera et al., 2015 , khatun et al., 2015 . future investigations of emerging infection outbreaks should consider using these more intensive strategies, at least in a subset of investigations, to improve our understanding of these infections and our public health response. according to institutional data policy of the international centre for diarrhoeal disease research, bangladesh (icddr,b), summary of data can be publicly displayed or can be made publicly accessible. to protect intellectual property rights of primary data, icddr,b cannot make primary data publicly available. however, upon request, institutional data access committee of icddr,b can provide access to primary data to any individual, upon reviewing the nature and potential use of the data. requests for data can be forwarded to: this work was supported by centers for disease control and prevention (cdc), atlanta, usa [cooperative agreement no: 5u01ci000628]. in addition, the government of bangladesh, canada, sweden and the uk provided core/unrestricted funding support for this work. the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. chikungunya virus outbreak hospital-associated outbreak of middle east respiratory syndrome coronavirus: a serologic, epidemiologic, and clinical description chikungunya outbreak ebola virus disease in west africa--the first 9 months of the epidemic and forward projections investigation of chikungunya fever outbreak in laguna bangladesh population and housing census 2011 added value of a household-level study during an outbreak investigation of salmonella serotype saintpaul infections is dengue vector control deficient in effectiveness or evidence?: systematic review and meta-analysis delivery complications and healthcare-seeking behaviour: the bangladesh demographic health survey chikungunya in europe: what's next? household transmission of 2009 influenza a (h1n1) virus after a school-based outbreak first identified outbreak of chikungunya in bangladesh laboratory diagnosis of chikungunya virus infections and commercial sources for diagnostic assays early appearance of neutralizing immunoglobulin g3 antibodies is associated with chikungunya virus clearance and long-term clinical protection an outbreak of chikungunya in rural bangladesh estimating potential incidence of mers-cov associated with hajj pilgrims to saudi arabia dynamics and control of ebola virus transmission in montserrado, liberia: a mathematical modelling analysis ebola virus outbreak investigation an epidemic of virus disease in southern province, tanganyika territory general description and epidemiology evaluating hospital-based surveillance for outbreak detection in bangladesh: analysis of healthcare utilization data gender differences in healthcare-seeking during common illnesses in a rural community of west bengal reconstruction of 60 years of chikungunya epidemiology in the philippines demonstrates episodic and focal transmission how social structures, space, and behaviors shape the spread of infectious diseases using chikungunya as a case study selection of important variables and determination of functional form for continuous predictors in multivariable model building seroprevalence and risk factors of chikungunya virus infection in mayotte the epidemic of zika virus-related microcephaly in brazil: detection, control, etiology, and future scenarios effect of ebola progression on transmission and control in liberia the authors have no competing interests to declare. j o u r n a l p r e -p r o o f key: cord-257073-dm80bxnd authors: akmatov, manas k.; krebs, stephan; preusse, matthias; gatzemeier, anja; frischmann, ursula; schughart, klaus; pessler, frank title: e-mail-based symptomatic surveillance combined with self-collection of nasal swabs: a new tool for acute respiratory infection epidemiology date: 2011-08-17 journal: int j infect dis doi: 10.1016/j.ijid.2011.07.005 sha: doc_id: 257073 cord_uid: dm80bxnd objective: we examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. methods: the study was conducted among a convenience sample of employees (n = 53) at a research institution (december 2009–april 2010). real-time data on the occurrence of acute respiratory symptoms and a nasal self-swab were collected prospectively, with automated weekly e-mails as a reminder mechanism. reverse transcription polymerase chain reaction (rt-pcr) was used to detect respiratory viral pathogens in the swabs. results: fifty-one out of 53 participants completed the study. the study design was well accepted. thirty (∼57%) participants reported at least one episode of acute respiratory infection and returned the nasal swab during the study period (eight participants reported two episodes). the majority had no difficulties taking the self-swab and preferred this to swabbing by study personnel. most participants obtained and returned the swabs within the recommended time. viral respiratory pathogens were detected in 19 of 38 swabs (50%), with coronaviruses 229e/nl63 and oc43 and rhinoviruses a and b constituting 17 positive swabs (89%). conclusions: combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. research on acute respiratory infections in human populations is limited by certain methodological difficulties. first, their acute nature makes a timely diagnosis difficult. second, symptoms are usually not unique for specific pathogens. these difficulties impede collecting epidemiologic (e.g., risk factors for acute respiratory infections) and clinical (e.g., the course and severity of infections) data, as well as biosamples for pathogen identification. in particular, the real-time collection of diagnostic specimens such as nasal or nasopharyngeal swabs during an acute respiratory infection season is necessary to link symptomatic data with specific pathogens. 1 therefore, there is an urgent need to develop epidemiologic research tools that ensure the timely detection of incident acute respiratory infections and the collection of diagnostic biosamples during the episode. most epidemiologic studies on acute respiratory infections have been based in medical settings or have been conducted in specific target populations such as trained medical personnel. data on the occurrence and severity of symptoms have been collected in a few studies only, either retrospectively, 2 usually at the end of an acute respiratory infection season, or prospectively, for instance by using diary-based questionnaires. 3, 4 recently, modern communication tools such as weekly e-mails 5 and internet-based questionnaires 6, 7 have been introduced in population-based studies to collect real-time data on respiratory infections. in a recent study of influenza infection, short message service (sms) was used in addition to e-mail. 8 the main limitation of these studies is the lack of pathogen identification during specific episodes of acute respiratory infections. nasal swabs for pathogen detection are usually collected by study personnel at the study site or in hospital. however, due to logistic problems and higher costs, this is difficult to organize in population-based studies with their inherently larger sample sizes. in several recent studies subjects were asked to obtain swabs from their own nares ('self-swabbing') to detect viral respiratory pathogens, but most of these studies were performed s u m m a r y objective: we examined the feasibility of combining communication by e-mail and self-collection of nasal swabs for the prospective detection of acute respiratory infections in a non-medical setting. methods: the study was conducted among a convenience sample of employees (n = 53) at a research institution (december 2009-april 2010). real-time data on the occurrence of acute respiratory symptoms and a nasal self-swab were collected prospectively, with automated weekly e-mails as a reminder mechanism. reverse transcription polymerase chain reaction (rt-pcr) was used to detect respiratory viral pathogens in the swabs. results: fifty-one out of 53 participants completed the study. the study design was well accepted. thirty ($57%) participants reported at least one episode of acute respiratory infection and returned the nasal swab during the study period (eight participants reported two episodes). the majority had no difficulties taking the self-swab and preferred this to swabbing by study personnel. most participants obtained and returned the swabs within the recommended time. viral respiratory pathogens were detected in 19 of 38 swabs (50%), with coronaviruses 229e/nl63 and oc43 and rhinoviruses a and b constituting 17 positive swabs (89%). conclusions: combining e-mail-based symptomatic surveillance with nasal self-swabbing promises to be a powerful tool for the real-time identification of incident cases of acute respiratory infections and the associated pathogens in population-based studies. ß 2011 international society for infectious diseases. published by elsevier ltd. all rights reserved. in healthcare environments. for instance, parents collected swabs from their symptomatic children when presenting for pediatric medical evaluation, 9 or nurses self-swabbed during symptomatic episodes in a study comparing two measures for the prevention of influenza transmission. 10 in the uk, swabs for the collection of nasal specimens were sent to individuals who contacted the health advice and information service ('nhs direct') because of influenzalike symptoms. 11 the only population-based study was conducted among parents who collected nasal swabs from their children at home. 12 thus, the feasibility of nasal self-swabbing for the detection of respiratory pathogens in population-based studies of adults remains to be demonstrated. moreover, little is known about whether any added benefit results when active symptomatic surveillance is conducted to ensure the timely self-collection of swabs during the time window in which causative pathogens are detectable. we therefore examined the feasibility of combining email-based active symptomatic surveillance with nasal selfswabbing for the detection of viral respiratory pathogens in a prospective study spanning one acute respiratory infection season. we conducted a prospective study among employees of the helmholtz centre for infection research (hzi) in braunschweig, germany, from december 2009 to april/may 2010. in december 2009, invitations to participate in the study were sent to all employees (age 18-69 years) through the internal e-mail system. this invitation contained a link to the institutional intranet where information about the study was made available. subjects not eligible for study participation were those vaccinated against seasonal influenza in the season 2009/2010, staff of the department of infection genetics (due to ethical considerations), and those who planned to leave braunschweig during the study period. the study was approved by the ethics committee of the state board of physicians of the german federal state of lower saxony. fifty-three participants responded to the invitation e-mail, corresponding to a response rate of approximately 12% ( figure 1 ). all subjects gave written informed consent before entering the study. at baseline (december 2009), information on sociodemographics (sex, age, education, profession, country of birth, number of individuals living in the household, etc.), contacts with animals, history of vaccination against influenza, and general health status was collected through a self-administered questionnaire. the pre-season blood sample was also obtained at this time. in april/may 2010 the study participants were reinvited to give the post-season blood sample and fill in a short questionnaire. every participant who completed the post-study questionnaire and blood sampling received a remuneration of 20 s. serum samples were stored at à70 8c. however, at the conclusion of the study it was decided to forgo the originally planned influenza hemagglutination inhibition assays because of the unexpectedly low incidence of influenza infection in germany during the study period. during january-march 2010 the participants were asked to take a swab from one of the anterior nares and return it to the study site as soon as possible if they had at least one of the following acute respiratory symptoms: sudden onset of stuffy or running nose, cough, sore throat, or fever >38 8c. they received instruction by a physician (s.k.) on how to perform the nasal swab. briefly, the swab was to be inserted into one nostril to a depth of 1-2 cm, rotated three times, and then placed into transport medium. two kits for nasal swabbing containing a regular flocked swab with molded breakpoint (copan, brescia, italy; product number 359c) and viral universal transport medium were given to the participants. during symptomatic surveillance, weekly automated e-mail messages were sent to the participants containing (1) a reminder to take a swab at the onset of at least one of the abovementioned symptoms and (2) instructions on how to collect, store, and return the swab. visual instructions on how to collect the swab were also available on the package. participants were instructed to store the self-collected swab in the refrigerator (+4 8c) until returning it, as soon as possible, to the study team. upon receipt at the study site, swabs were held at à70 8c until analysis. because of the low response rate, we conducted a non-responder survey in april 2010 ( figure 1 ). the survey was done through a selfadministered questionnaire, which was sent via the internal e-mail system. to maintain anonymity, responding individuals (n = 142) were asked to return the completed questionnaire by in-house mail. among other items, information was collected regarding reasons for not participating in the study and the occurrence of respiratory infections during the study period. data were described as percentages for categorical variables and medians with range for continuous variables. differences between groups were tested with the chi-square test (for categorical variables) and the mann-whitney u-test (for continuous variables). overall, there were only minor differences between the participants and the non-responders (table 1 ). participants were slightly younger than non-responders (p = 0.03); approximately 17% of the participants and 9% of the non-responders were born outside germany (p = 0.09). about half of the subjects in both groups had a university degree (including universities of applied sciences). there was a slightly higher proportion of smokers among the responders (p = 0.02). reasons for not participating were: 'did not meet inclusion criteria' ($31%), 'no time' ($27%), 'absent because of illness or vacation' ($16%), 'did not read the invitation e-mail' ($12%), 'fear of blood draw' ($7%), 'concern of inadequate data protection', 'no interest' ($6% each), and 'information about the study was unclear' ($5%) (subjects were allowed to give more than one reason). out of 53 participants, 30 provided 38 nasal swabs during the symptomatic follow-up period (eight individuals had two symptomatic episodes). thus, the clinical attack rate of acute respiratory infection, based on at least one reported symptom, was 53.6% (table 2 ). about 38% of the participants reported at least two, 18% at least three, and 9% at least four symptoms. similar proportions of non-responders reported three or more symptoms. however, the proportion of individuals who reported mild infections (one or two symptoms) was significantly lower among the non-responders than the study participants. fifty-one out of 53 participants completed all aspects of the study. one participant had to leave the study because he moved away and one participant was lost to follow-up. nearly all study participants found the study design acceptable (table 3) , and the vast majority of participants would participate again in such a study. only six percent found a weekly e-mail reminder to take the swab unacceptable. the majority of those who collected a nasal swab reported no difficulties in self-swabbing. only one participant reported difficulties opening the swab tube. about 15% felt discomfort while performing the swab. all participants who reported acute respiratory symptoms during the period of symptomatic surveillance (n = 30) selfcollected the nasal swab. eight subjects reported two episodes of respiratory infections, and all eight returned two swabs. at the end of the study period one person reported that he/she took the swab but did not bring it to the study center. the reason stated was ''i forgot to bring the swab to the study center''. of these participants with symptoms of an acute respiratory infection, 85.7% collected the swab within the first 3 days of the onset of symptoms. one person collected the swab on the sixth day. half of the participants brought the swab to the study center on the day of taking it. the maximum time between swab collection and delivery was 2 weeks. respiratory pathogenic viruses were detected by reverse transcription polymerase chain reaction (rt-pcr) in about 50% of the swabs (table 4) , and the most frequently recorded ones were human coronaviruses 229e/nl63 (8/38 swabs, $21%) and oc43 (5/ 38 swabs, $13%). co-infections were detected in two specimens. influenza viruses were not detected. there were no differences in the proportion of positive (for any viruses) and negative swabs in terms of participant sex, age, and level of education. also, there were no differences in the time elapsed between the onset of symptoms and self-swabbing (figure 2a) or the time between selfswabbing and arrival of the swab at the study center ( figure 2b ). likewise, we did not detect any effects on viral detection when we controlled for potential effects of each variable (time (change per one day) between symptoms and swabbing, adjusted odds ratio (aor) 0.98, 95% confidence interval (ci) 0.50-1.93; time between swabbing and delivery, aor 0.96, 95% ci 0.76-1.21). we tested the feasibility of combining real-time symptomatic surveillance with nasal self-swabbing for the prospective collection of epidemiologic and virological data on acute respiratory infections. in the pre-analytical phase, this novel approach turned out to be highly feasible in that acceptance, satisfaction, compliance, and timeliness of logistics were high. notably, more than 90% of the participants who self-swabbed reported that the swab was easy to obtain and that they preferred self-collection to collection by study personnel. the reason for this high degree of satisfaction may be that self-swabbing reduces duration and frequency of contact with study personnel as well as travel to a study site. the resulting greater convenience would very likely impact positively on compliance in any largescale prospective study. another important finding of the presented study is that neither the time between onset of symptoms and self-swabbing nor the time between selfswabbing and specimen arrival at the laboratory influenced the viral detection rate. this agrees well with results from a study in the uk, 11 and is noteworthy, since in population-based studies employing self-swabbing, shipping time needs to be included in the time between swab collection and expected arrival of the specimen at the study center. factors other than time that could not be addressed in this study may influence the viral detection rate. one obvious candidate is the swabbing technique. the study physician instructed the participants in a standardized manner in the proper application of the technique. we do not believe that an inadequate technique impacted negatively on the rate of pathogen detection, since the detection rate of 50% recorded by us corresponds to what has been reported in other studies employing staff-collected swabs and similar detection technology. 13 also, two recent studies showed that there were no differences in pathogen detection between self-and staff-collected swabs. 14, 15 another factor that may influence the detection rate is the type of nasal swab used for specimen collection. recently, smieja et al. developed a flocked nasal mid-turbinate swab and compared it with the gold standard (e.g., rayon nasal and nasopharyngeal swabs). the mid-turbinate swab turned out to provide better results (based on epithelial cell counts) than the gold standard. 16 we used a regular flocked swab. thus, using the mid-turbinate flocked swab might have resulted in a higher detection rate in our study. the non-responder survey allowed us to compare prospectively (participants) and retrospectively (non-responders) collected data on acute respiratory infection symptoms, and it revealed that the prospective approach resulted in a higher rate of detection of mild infections. thus, one immediate strength of using active symptomatic surveillance in population-based studies on acute respiratory infections would be the more efficient identification of individuals with reduced susceptibility to infection, which would constitute an invaluable asset for large-scale studies on genetic determinants of infection susceptibility and resistance in humans. in such a study, using self-swabbing instead of swabbing by study personnel to detect specific pathogens would be immensely attractive due to its anticipated lower cost. indeed, expenses for personnel and logistics were estimated to be 80% less if self-swabbing was used instead of swabbing by study personnel. 17 previous methods of active symptomatic surveillance have been, for example, weekly telephone calls 18 or daily symptom diaries. 19 however, these methods might be costly and have lower compliance rates. limitations not addressed above include the representativeness of the study population. for instance, we had higher-thanexpected proportions of female ($75%) and highly educated subjects ($50%). moreover, due to working in a research institution, the participants could be expected to be more receptive to the study design than the general population. since e-mail has become the primary tool of communication in professional work environments, including our institution, the population sampled for the present study may have a higher acceptance of modern communication tools than the general population. further studies are needed regarding the use of electronic communication methods in population-based studies, particularly those targeting the less educated and the elderly. lastly, due to the unexpected near absence of influenza infection during the study period, we could not evaluate the usefulness of the study design for the detection of influenza infection. indeed, considering that upper respiratory symptoms occur only in about 60% and fever in about 35% of episodes of influenza infection, 20 inclusion of surveillance questions about other influenza-associated symptoms (e.g., myalgia or headache) would likely increase the efficiency of screening for influenza infection with e-mail-based surveillance. combining e-mail-based active symptomatic surveillance with self-collection of nasal swabs ensured prospective, accurate collection of data on incident episodes of acute respiratory infections and timely sample collection for the detection of respiratory pathogens. it promises to be an efficient and cost-effective approach in population-based studies on the epidemiology of respiratory infections. beyond the influenza-like illness surveillance: the need for real-time virological data incidence and recall of influenza in a cohort of glasgow healthcare workers during the 1993-4 epidemic: results of serum testing and questionnaire a children's acute respiratory illness scale (carifs) predicted functional severity and family burden the effect of giving influenza vaccination to general practitioners: a controlled trial internet-based monitoring of influenza-like illness (ili) in the general population of the netherlands during the 2003-2004 influenza season internet-based monitoring of influenza-like illness in the general population: experience of five influenza seasons in the netherlands internet-based surveillance of influenza-like-illness in the uk during the 2009 h1n1 influenza pandemic seasonal influenza risk in hospital healthcare workers is more strongly associated with household than occupational exposures: results from a prospective cohort collection by trained pediatricians or parents of mid-turbinate nasal flocked swabs for the detection of influenza viruses in childhood surgical mask vs n95 respirator for preventing influenza among health care workers: a randomized trial monitoring the emergence of community transmission of influenza a/h1n1 2009 in england: a cross sectional opportunistic survey of self sampled telephone callers to nhs direct parent-collected respiratory specimens-a novel method for respiratory virus and vaccine efficacy research multiplex real-time pcr for detection of respiratory tract infections evaluation and clinical validation of an alcohol-based transport medium for preservation and inactivation of respiratory viruses selfcollected mid-turbinate swabs for the detection of respiratory viruses in adults with acute respiratory illnesses development and evaluation of a flocked nasal mid-turbinate swab for self-collected respiratory virus diagnostic testing self-collected nasal swabs to detect infection and colonization: a useful tool for population-based epidemiological studies? effectiveness of influenza vaccine in health care professionals: a randomized trial community epidemiology of human metapneumovirus, human coronavirus nl63, and other respiratory viruses in healthy preschool-aged children using parentcollected specimens time lines of infection and disease in human influenza: a review of volunteer challenge studies we would like to thank the participants for their kind participation in the study. we thank prof. udo buchholz (robert koch institute, berlin, germany) for helpful comments on the study design and a critical reading of the manuscript. this work was supported with intramural funds from the helmholtz association (program infection and immunity).conflict of interest: the authors declare that they have no competing interests. key: cord-275250-ilmgy7ce authors: xia, yong; hong, honghai; feng, yao; liu, meiling; pan, xingfei; chen, dexiong title: dynamics of antibodies to sars-cov-2 in a case with sars-cov-2 infection date: 2020-05-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.042 sha: doc_id: 275250 cord_uid: ilmgy7ce nan to the editor: covid-19, caused by sars-cov-2, has been worldwide reported [1] . to date, the diagnosis of sars-cov-2 infection is dependent on detecting nucleuic acid of sars-cov-2 by qrt-pcr or by next-generation sequencing (ngs) [2] . in clinical practice, some highly suspected cases had negative results for nucleic acid of sars-cov-2 [3] . in the present study, we evaluated whether detecting antibodies to sars-cov-2 could be as a diagnostic marker for sars-cov-2 infection. a 29-year-old woman, had fever, no cough and fatigue on feb 9, 2020. on feb 12, she was referred to our hospital, because her mother was diagnosed as covid-19. nasopharyngeal swabs and anal swabs were collected and were assayed nucleic acid of sars-cov-2. peripheral blood samples were collected from the patient on feb 14, 17, and 20, respectively. four igg/igm antibodies detection kits (manufactured by company a, guangzhou darui biotechnology co., ltd; company b, zhuhai livzon diagnostics inc.; company c, beijing hotgen biotech co., ltd; company d, shenzhen new industries biomedical engineering co., ltd., respectively) were used to detect antibodies to sars-cov-2. colloidal gold method was used in kits a, b and c, while chemiluminescence method was used in kit d. kit c was coated with spike (s) and nucleocapsid (n) proteins of sars-cov-2. only n protein was coated in kits a, b and d, respectively. blood routine on admission showed lymphocyte counts were not lowered. on feb 15, chest ct images showed typical characteristics of covid-19. nasopharyngeal swabs and anal swabs were collected six times, and both were negative for sars-cov-2. furthermore, none of sars-cov-2 and other pathogens was found in the collected sputum samples tested by ngs. as shown in table 1 , on feb 14, reactivity to igm/ igg antibodies was very weak and invisible to the naked eye by using kit a, c. reactivity to igm antibody was positive and visible to the naked eye by using kit b. igm and igg antibodies had been assayed by using kit d, and igm and igg antibody levels were 0.62 au/ml, 2.41 au/ml, respectively (normal igm and igg <1.1 au/ml). on feb 17, reactivity to igg antibody was significantly positive, but reactivity to igm antibody was still weak by using kit a. reactivity to igm antibody was obviously positive by using kit b. igm and igg antibody levels were 0.74 au/ml, 6.90 au/ml, respectively. however, none of antibodies was detected by using kit c. on feb 20, reactivity to igm and igg was higher than that detected by using kit a on feb 17. reactivity to igm was also higher than that detected by using kit b and c on feb 17, respectively. furthermore, igm and igg antibody levels were 0.92 au/ml, 13.46 au/ml, respectively, which was higher than that detected by using kit d on feb 17 (figure 1 ). in the present study, igg/igm antibodies to specific proteins of sars-cov-2 were found in blood sample of the patient and gradually increased. because covid-19 is a newly emerged disease, the patient with either positive for igm or igg antibodies to sars-cov-2 should be considered as the presence of sars-cov-2 infection. so we believe that positive for igm or igg antibodies could be a marker to diagnosis of sars-cov-2 infection no matter the results of testing nucleic acid. dynamically detecting igg and igm antibodies to virus was very important to the diagnosis of viral infections [4, 5] . our results showed that igm or igg antibodies detected by different kit were gradually increased (table 1, figure 1 ). this implied that antibody to sars-cov-2 actually existed in the patient. although igm antibody level detected by kit d was increased, it was still note: n, nucleocapsid proteins of sars-cov-2; s, spike proteins of sars-cov-2. diagnosis and treatment of pneumonitis caused by new coronavirus (trial version 6) comparison of the clinical characteristics between rna positive and negative patients clinically diagnosed with 2019 novel coronavirus pneumonia zhonghua jie he he hu xi za zhi key: cord-280627-dfnc9g2c authors: wang, xiong; tan, li; wang, xu; liu, weiyong; lu, yanjun; cheng, liming; sun, ziyong title: comparison of nasopharyngeal and oropharyngeal swabs for sars-cov-2 detection in 353 patients received tests with both specimens simultaneously date: 2020-04-18 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.023 sha: doc_id: 280627 cord_uid: dfnc9g2c abstract background since the outbreak of coronavirus disease (covid-19) in wuhan in december 2019, by march 10, 2020, a total of 80,932 confirmed cases have been reported in china. two consecutively negative rt-pcr test results in respiratory tract specimens is required for the evaluation of discharge from hospital, and oropharyngeal swabs were the most common sample. however, false negative results occurred in the late stage of hospitalization, and avoiding false negative result is critical essential. methods we reviewed the medical record of 353 patients who received tests with both specimens simultaneously, and compared the performance between nasopharyngeal and oropharyngeal swabs. results of the 353 patients (outpatients, 192; inpatients, 161) studied, the median age was 54 years, and 177 (50.1%) were women. higher positive rate (positive tests/total tests) was observed in nasopharyngeal swabs than oropharyngeal swabs, especially in inpatients. nasopharyngeal swabs from inpatients showed higher positive rate than outpatients. nasopharyngeal swabs from male showed higher positive rate than female, especially in outpatients. detection with both specimens slightly increased the positive rate than nasopharyngeal swab only. moreover, the consistency between from nasopharyngeal and oropharyngeal swabs were poor (kappa=0.308). conclusion in conclusion, our study suggests that nasopharyngeal swabs may be more suitable than oropharyngeal swab at this stage of covid-19 outbreak. in december 2019, the coronavirus disease (covid-19) occurred in wuhan, china, and spread rapidly to become public health emergency of international concern, which is caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection 1, 2 . up to march 2, 2020, a total of 80,174 confirmed cases including 49,315 in wuhan have been reported in china. the typical symptoms of covid-19 include: fever, dry cough, fatigue, sputum production, and shortness of breath. all people are susceptible to covid-19, including infants and children [3] [4] [5] , and human to human transmission has been confirmed 6 . no specific drugs have been identified for covid. the currently widely used treatments include, antiviral treatment such as arbidol and ribavirin, antibiotics, corticosteroid, noninvasive or invasive ventilation, and extracorporeal membrane for critically ill patients [7] [8] [9] . multiple platforms are under development for covid-19 vaccines at pandemic speed 10 . the diagnosis of covid-19 is mainly based on typical symptoms, bilateral involvement on chest radiographs, and exposure to infected patients, and confirmed by positive nucleic acid test of sars-cov-2 from numerous types of specimens. reverse-transcriptase-polymerase-chain-reaction (rt-pcr) is the most common method for sars-cov-2 detection by targeting the orf1ab, n, or e genes. oropharyngeal and nasopharyngeal swabs were most frequently used samples 11 . however, negative oropharyngeal and nasopharyngeal swabs could not rule out covid-19, as some patients got positive sars-cov-2 from other types of specimen, including bronchoalveolar lavage fluid j o u r n a l p r e -p r o o f (balf), anal swab, stool, and urine 12, 13 . false negative sars-cov-2 occurred, and positive rt-pcr test results of sars-cov-2 were observed in patients recovered from covid-19 14 . evaluation of different types of specimen may promote the positive rate (positive tests/total tests), and be helpful for the decision of discharge from hospital. since february 16 2020, sars-cov-2 nucleic acid detections using both nasopharyngeal and oropharyngeal swabs have been performed simultaneously for some patients in our hospital. we reviewed the medical record from february 16, 2020 to march 2, 2020, and compared the performance between nasopharyngeal and oropharyngeal swabs in sars-cov-2 detection from 353 patients who received tests with both specimens simultaneously. covid-19 was diagnosed based on the who interim guidance 12 . patients who showed covid-19 like symptoms, such as fever, cough, and fatigue, were initially screened in community hospitals for fever and chest x-ray. if patients had fever or chest x-ray abnormality, they would be further admitted to the fever clinic as outpatient in designated hospitals for covid-19 to get sars-cov-2 rt-pcr test and chest computed tomography (ct) scanning. our hospital was one of the designated hospitals for covid-19. all inpatients had positive result in sars-cov-2 rt-pcr test before hospitalization. some of the inpatients in our hospital were transferred from other hospital, as our hospital was one of the designated hospitals for severe and very severe covid-19 patients. a total of 353 patients were collected in this study, including 192 outpatients and 161 inpatients. this study was approved by tongji hospital ethics committee. a nasopharyngeal swab was collected from single nostril according to a detailed video in a previously published study 15 . a oropharyngeal swab was collected from both sides of throat according to a published video by chinese society of laboratory medicine (http://www.cslm.org.cn/cn/news.asp?id=74.html). a nasopharyngeal swab and an oropharyngeal swab for each patient were taken at the same time as each other, and sent to sars-cov-2 rt-pcr test simultaneously. data including age, sex, and sars-cov-2 rt-pcr results were extracted from electronic medical records up to march 2, 2020. only the cases who received tests with both nasopharyngeal and oropharyngeal swabs simultaneously were included in our study. laboratory confirmation of sars-cov-2 was performed in the department of laboratory medicine using rt-pcr. respiratory tract specimen was suggested for sars-cov-2 rt-pcr test, including nasopharyngeal and oropharyngeal swab, sputum and bronchoalveolar lavage fluid (balf). oropharyngeal swab was widely used in the beginning of covid-19 outbreak. specimens were collected and stored in a collection tube with 5 ml virus preservation solution. rna was isolated with tianlong pana9600 automatic nucleic acid extraction system (tianlong, xi'an, china). the data were presented as medians with interquartile (iqr) ranges and range. categorical variables were analyzed using the χ2 or fisher's exact test. correlation and consistency were analyzed using mcnemar test and kappa coefficient. all analyses were done with spss 16. p value <0.05 was considered statistically significant. of the 353 patients (outpatients, 192; inpatients, 161) studied, the median age was 54 years (range, 20 to 88 years), and 177 (50.1%) were women. the positive rates from total, outpatient, and inpatient, were 19.0% vs 7.6%, 7.3% vs 6.3%, and 32.9% vs 9.3% in nasopharyngeal and oropharyngeal swabs, respectively ( table 1 ). the positive rates from both nasopharyngeal and oropharyngeal swabs in outpatient decreased sharply to less than 10%, much lower than early stage of covid-19 outbreak 11 . the combined positive rate was calculated if either result from nasopharyngeal and oropharyngeal swabs was positive, and it increased to 21.5%, 9.9%, and 35.4% in total, outpatient, and inpatient respectively, slightly higher those from nasopharyngeal swabs, j o u r n a l p r e -p r o o f which was 19.0%, 7.3%, and 32.9%, respectively. moreover, among the inpatient group, the positive rate was quite different between nasopharyngeal and oropharyngeal swabs, 32.9% vs 9.3%. as all the 49,315 infected patients must be hospitalized and evaluated for discharge from hospital based on the result of sars-cov-2 nucleic acid detection, oropharyngeal swab may cause remarkable false negative results and lead to the discharge of infected patients from hospital. male patients showed significantly higher positive rate in total male population than total female population, and in male outpatients than female outpatients from nasopharyngeal but not oropharyngeal swabs (table 2) . among the 27 positive results in oropharyngeal swabs, 18 cases were also positive in nasopharyngeal swabs, accounting for 66.7%, and the remaining 9 patients included 5 outpatients and 4 inpatients. among the 67 positive results in nasopharyngeal swabs, 49 cases were negative in oropharyngeal swabs, accounting for 73.1%. the consistency between from nasopharyngeal and oropharyngeal swabs were poor (table 3 ). two consecutively negative rt-pcr test results in specimens from respiratory tract separated by at least 1 day is required for the evaluation of discharge from hospital, and oropharyngeal swab samples were still the most common sample 3 . however, false negative result may occur in the late j o u r n a l p r e -p r o o f stage of hospitalization. positive rt-pcr test results were found in recovered patients two weeks after discharge 14 . live sars-cov-2 has been found from stool in some patients 12 . in our study, positive rt-pcr test results showed quite difference between nasopharyngeal and oropharyngeal swabs. 73.1% of nasopharyngeal positive cases were negative in oropharyngeal swab, indicating false negative results may occur using oropharyngeal swab only. these results suggest that nasopharyngeal swabs showed higher positive rate than oropharyngeal swabs for sars-cov-2 detection, and oropharyngeal swabs may result in a worryingly high false negative rate. the reduced susceptibility of females to covid-19 had been observed in our study, consistent with previous studies 16 . moreover, a recent meta-analysis found that among the included 50,488 chinese patients, male accounted more than female with an odds of 1.13 17 . in conclusion, nasopharyngeal swabs showed higher positive rate than oropharyngeal swabs. our study suggests that nasopharyngeal swabs may be more suitable than oropharyngeal swab at this late stage of covid-19 outbreak. covid-19 control in china during mass population movements at new year initiation of a new infection control system for the covid-19 outbreak characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72314 cases from the chinese center for disease control and prevention china national clinical research center for respiratory d, national center for children's health bc, group of respirology cpscma, chinese medical doctor association committee on respirology p, china medicine education association committee on p, chinese research hospital association committee on p, chinese non-government medical institutions association committee on p, china association of traditional chinese medicine cocsh, medicine r, china news of drug information association cocssm, global pediatric pulmonology a. diagnosis, treatment, and prevention of 2019 novel coronavirus infection in children: experts' consensus statement novel coronavirus infection in hospitalized infants under 1 year of age in china clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study. the lancet respiratory discovering drugs to treat coronavirus disease 2019 (covid-19) developing covid-19 vaccines at pandemic speed. the new england journal of medicine clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in who-china joint mission. report of the who-china joint mission on coronavirus disease negative nasopharyngeal and oropharyngeal swab does not rule out covid-19 positive rt-pcr test results in patients recovered from covid-19 h1n1 influenza a disease--information for health professionals epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study sex differences in severity and mortality among patients with covid-19: evidence from pooled literature analysis and insights from integrated bioinformatic analysis key: cord-275191-lgze4zex authors: al-sadeq, duaa w.; nasrallah, gheyath k. title: the incidence of the novel coronavirus sars-cov-2 among asymptomatic patients: a systematic review date: 2020-07-02 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.098 sha: doc_id: 275191 cord_uid: lgze4zex background: the recent outbreak of the coronavirus disease 2019 (covid‐19) has quickly spread globally since its discovery in wuhan, china, in december 2019. a comprehensive strategy, including surveillance, diagnostics, research, and clinical treatment is urgently needed to win the battle against covid-19. recently, numerous studies reported the incidence of sars-cov-2 in asymptomatic patients. yet, the incidence and viral transmission from the asymptomatic cases are not apparent yet. aim: this study aims to systematically review the published literature on sars-cov-2 in the asymptomatic patients to estimate the incidence of covid-19 among asymptomatic cases, as well as describe its epidemiological and clinical significance. method: the literature was searched through four scientific databases: pubmed, web of science, scopus, and science direct. results: a total of 63 studies satisfied the inclusion criteria where the majority of the reported studies were from china. however, there was a lack of sars-cov-2 epidemiological studies from several countries worldwide, tracing the actual incidence of covid-19, especially in asymptomatic patients. studies with a large sample size (n>1000) estimated that percentage of people contracting sars-cov-2 and are likely to be asymptomatic ranges from 1.2-12.9%. however, the other studies with a smaller sample size reported a much higher incidence and indicated that up to 87.9% of covid-19 infected individuals could be asymptomatic. most of these studies indicated that asymptopatics are a potential source of infection to the community. conclusion: this review highlighted the need for more robust and well-designed studies to better estimate covid-19 incidence among asymptomatic patients worldwide. the early identification of the asymptomatic cases, as well as monitoring and tracing close contact, could help in mitigating the spread of covid-19. infectious diseases impose a major health threat globally, leading to 15 million deaths annually [1] . although the percentage of mortality due to infectious diseases has declined, numerous new infectious diseases have been identified and reported recently. the novel coronavirus disease , caused by the sars-cov-2 virus, was firstly identified in wuhan, china, in late december 2019 as an outbreak of unusual viral pneumonia [2] . later, the world health organization (who) declared a public health emergency worldwide, and the total number of infected cases reached 4.4 million by may 2020 [3] . consequently, educational institutions, business centers, public transport, and other social interaction were locked down points to prevent the spread of covid-19 and ease the burden on health facilities. sars-cov-2 is an enveloped positive-sense single-stranded rna virus with six open reading frames (orfs) that codes for structural proteins, including surface (s), envelope (e), membrane (m), and nucleocapsid n proteins [4] . based on the genomic structures and phylogenetic analysis of sars-cov-2, the virus belongs to genera betacoronavirus, which includes sars-cov and mers-cov. yet, sars-cov-2 has differences in its genomic that can influence its pathogenesis. the most effective approach to prevent and mitigate the adverse consequences of this viral pandemic requires the development of effective surveillance programs, incorporated with laboratory preparedness. diagnostic laboratory tests play a significant role in the rapid and accurate detection of new viruses [5, 6] . currently, real-time reverse-transcription polymerase chain reaction (rt-pcr) testing is the main technique used for the diagnosis of covid-19. however, false-negative rt-pcr results occur in up to 30% of covid-19 patients [7] [8] [9] . this could be due to the collection of inappropriate or insufficient sample, inaccurate conditions of sample transportation and storage, as well as collecting the sample too late in the disease process. on the other hand, serology testing could cover this gap since detecting sars-cov-2 igg antibodies could indicate recovery or immunity from covid-19 infection. besides, igm could be detected in the acute phase of infections. although, manual enzyme-linked immunoassay (elisa) kits could be subjected to non-specific binding and cross-reactivity with other coronaviruses such as mers-cov and sars-cov-1, most commercially available antibodies utilize lateral flow assays (lfa) [10] . however, recently elisa and automated-based assays were also introduced. the diagnostic performance, including sensitivity and specificity, of these assays, were better than the lfa [11] . it worth mentioning that there is a high percent of covid-19 asymptomatic patients who could transmit the infection to all communities. for instance, the asymptomatic ratio of covid-19 was estimated to be 41.6% of japanese individuals who were evacuated from china [12] . similarly, 72% of people infected with covid-19 on board the diamond princess cruise ship were asymptomatic [13] . however, the extent of viral transmission from the asymptomatic cases is not clear yet. the positive rt-pcr results only imply the potential infectivity. a prospective study was published on march 28 in which the viral load and clinical manifestations of 2,147 close contacts of symptomatic and asymptomatic covid-19 cases were followed up [15] . the study concluded that the virus infection rate of close contacts with asymptomatic patients was 4.11%. since the transmission ability of asymptomatic individuals should not be ignored, it was of interest to conduct a systemic review to paint a picture of the current status and incidence of sars-cov-2 in asymptomatic patients. therefore, this study would give significant insights into covid-19 infection and help health authorities to determine the need for social distancing close contact restrictions in specific areas or populations. j o u r n a l p r e -p r o o f we conducted a systematic review of all literature published on covid-19 in the asymptomatic patients using four databases: pubmed, web of science, scopus, and sciencedirect. the search covered all literature within the databases up to april 2020. the databases were queried with the keywords: "covid-19", "sars-cov-2", "seroprevalence", and "asymptomatic" to ensure complete coverage of all literature. the four databases were searched without filters. therefore, results that were letters and commentaries were also included. all retrieved citations were imported into endnote x8, and duplicates were removed using the endnote x8 built-in "find duplicates" feature. finally, the titles and abstracts of the remaining citations were screened to remove any irrelevant articles. the following inclusion criteria were used in study selection: (i) published in a peerreviewed journal, letters, case reports, and commentaries (ii) articles studying the covid-19 infection in asymptomatic patients, and (iii) articles published in english or at least with an abstract in english. a schematic of the search strategy and study selection process is shown in figure 1 . besides, studies that reported the coinfection of covid-19 with other viruses as well as comorbidities, such as cancer and cystic fibrosis, were also included in this study. no exclusion criteria were followed unless the studies did not report the incidence of sars-cov-2 in asymptomatic patients, published in a non-english language, or do not have full-text access. the studies included in this systematic review were analyzed two times by the same individual to ensure accurate capture of the information. the analyzed data included the incidence the search yielded 505 studies, of which 370 citations remained after removing duplicates ( figure 1 ). after screening the titles, abstracts, and keywords, 312 citations were excluded. the removed citations included irrelevant studies. the remaining 67 citations were screened against the eligibility criteria. of these, one study was removed due to the unavailability of full-text access. furthermore, three studies were removed two for being published in languages other than english with no english abstract. the remaining 63 studies were included in this study for further analysis, and they consisted of letters to the editor, commentaries, case reports as well as research studies. the reviewed studies covered sars-cov-2 incidence worldwide. country-wise, the majority of the studies were from china (n = 44) and included different provinces such as wuhan, shenzhen, guangzhou, beijing, shanghai, hunan, nanjing, guangdong, anhui, hubei, zhejiang, jinan, and hefei ( table 1 ). the remaining studies were published in japan (n = 2), italy (n = 3), germany (n = 1), iran (n = 2), and usa (n = 6), which included studies from texas, washington, and new york. however, there was a lack of sars-cov-2 epidemiological studies from several countries worldwide, tracing the actual incidence of covid-19, especially in asymptomatic patients. looking at all the included studies with a large sample size (n>1000 cases), these studies (table 1 , highlighted with bold text) estimated that percentage of people contracting sars-cov-2 and are likely to be asymptomatic range from (1.2-12.9%). however, the other studies with a smaller sample size (n<1000) reported a much higher incidence and indicated that up to 87.9% of covid-19 infected individuals could be asymptomatic ( table 1) . most of these estimates were based on rt-pcr results. on the other hand, the estimated seroprevalence of antibodies to sars-cov-2 was reported to be higher. for instance, a study that was performed on 2,857 blood donors from rio de janeiro showed 23.7% of igm positive cases, 11.4% of igg positive cases, while both igm and igg was detected in 64.9% [16] . this is could due to the limitation of the nasal swab since the pcr diagnostic could be negative though antibody detection is positive. in fact, this finding was reported in a study where four subjects out of 317 asymptomatic participants had negative pcr diagnostic, while antibody testing was positive [17] . therefore, relying only on molecular testing could significantly underestimate the seroprevalence sars-cov-2, especially in asymptomatic individuals. j o u r n a l p r e -p r o o f the spread of covid-19 is an emerging condition with pandemic potential that threatens all countries. over the last four months, more than three million cases of covid-19 have been confirmed worldwide. numerous epidemiologic investigations identified an association with respiratory droplet transmission. yet, understanding of the transmission risk is incomplete. it worth mention that covid-19 asymptomatic individuals may pose a significant public health threat. the majority of these patients might be unaware of their disease and, therefore, not isolate themselves or seek treatment. consequently, unknowingly transmit the virus to others. to the best of our knowledge, this is the first systematic review study that investigated the incidence of sars-cov-2 in asymptomatic patients. a total of 63 out of 505 screened studies reporting covid-19 asymptomatic patients were included in this review. epidemiological data, clinical laboratory results, ct image findings, as well as the medical and contact history of the patient are critical knowledge that should be carefully studied when a new infectious disease emerged [59] . although asymptomatic patients with sars-cov-2 were uncommon, studies showed that the prevalence of sars-cov-2 in asymptomatic patients is underestimated and might increase. for instance, a review paper showed the rate of asymptomatic individuals with the middle east respiratory syndrome coronavirus (mers-cov) ranged from 0% to 28.6% [60] . besides, it was reported that 75% of covid-19 infected individuals could be asymptomatic [55] . [19] . similarly, a study reported in china (wuhan) showed a 3-years old male asymptomatic patient with positive rt-pcr for sars-cov-2 and normal lymphocyte counts and chest ct images [20] . it is unknown yet the reason of having a benign clinical course and low incidence of covid-19 in children compared to adults. a proposed hypothesis suggested that it might be due to the low expression of ace2 receptors, high plasticity of their immune system, or to the exposure of other coronaviruses which are generally common in kids [61, 62] . besides, children may play a major role in community-based viral transmission. for instance, it was reported that viral shedding in the stool sample could persist for several weeks after diagnosis [63, 64] . consequently, it poses a threat of viral transmission through the fecal-oral route, particularly for infants and children who are not toilet trained. most of the reported covid-19 cases in children were due to close contact with family members with sars-cov-2 infection (table 1 ). many experts believe that undetermined asymptomatic cases of covid-19 infection could be an important source of contagion [41] . therefore, the early identification of the asymptomatic cases, as well as monitoring and tracing close contact, could help in mitigating the spread of covid-19 infection. another factor that increases the asymptomatic rate of covid-19 is the inaccuracy of diagnostic testing. for instance, a recent article highlighted key important steps to be considered when designing seroprevalence studies, as well as experts' opinion on the recent studies. a major concern raised about the recently published results was the type of antibody test used since most of them inaccurate to support the conclusions [65] . it was reported that the manual elisa kits are subject to cross-reaction with other coronaviruses such as sars-cov-1 and mers-cov [10] . besides, some of the included studies reported that the patients were positive for sars-cov-2 igg, which suggested that the patient was an asymptomatic sars-cov-2 carrier. the differential use of serology for confirming acute infection is not appropriate without the additional collaboration of results. therefore, combining both molecular and serological testing would be the best approach to accurately estimate the prevalence of covid-19 infection, especially if the patient is at later stages of the infection and does not show symptoms [68] . although governments in many countries are planning to conduct largescale seroprevalence surveys, many laboratories try to rely on well-established and validated lab tests, rather than rapid tests. the latter is based on blood collected from finger pricks to detect sarsfunding: this work is supported by qnrf grant no. rrc-032 grant was given to g.k.n. we would like also to thank qatar national library (a member of qatar foundation) for sponsoring the publication fees of this article. the work presented in this manuscript does not involve 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kamat, sadettin; demirok, berna; surmeli, cemile dilsah; calik, mustafa; cavus, zuhal; esatoglu, sinem nihal title: performance of pneumonia severity index and curb-65 in predicting 30-day mortality in patients with covid-19 date: 2020-06-14 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.038 sha: doc_id: 305782 cord_uid: gnzwe2z2 abstract objective the aim of the study was to analyze the usefulness of the curb-65 and pneumonia severity index (psi) in predicting 30-day mortality in patients with covid-19 and to identify other factors associated with higher mortality. methods a retrospective study was performed at a pandemic hospital in istanbul, turkey and 681 laboratory-confirmed patients with covid-19 were included. data on characteristics, vital signs and laboratory parameters were recorded form electronic medical records. we used receiver operating characteristic analysis to quantify the discriminatory abilities of the prognostic scales. univariate and multivariate logistic regression analyses were performed to identify other predictors of mortality. results higher crp levels were associated with an increased risk for mortality (or:1.015, 95% ci 1.008 to 1.021, p < 0.001). the psi performed significantly better than the curb-65 (auc: 0.91, 95% ci 0.88-0.93 vs auc:0.88, 95% ci:0.85-0.90; p = 0.01) and the addition of crp levels to psi did not improve the performance of psi in predicting mortality (auc: 0.91, 95% ci 0.88-0.93 vs auc:0.92, 95% ci:0.89-0.94; p = 0.29). conclusion in a large group of hospitalized patients with covid-19, we found that psi performed better than curb-65 in predicting mortality. adding crp levels to psi did not improve the 30-day mortality prediction. the novel coronavirus disease 2019 , caused by the severe acute respiratory syndrome coronavirus-2 (sars-cov-2), has become a major health concern worldwide. according to the world health organization, as of may 31, 2020, there were 5.934.936 confirmed cases and 367.166 deaths (who, 2020) . respiratory failure is the leading cause of mortality in patients with covid-19 (ruan et al. 2020) . myocardial injury, kidney or liver injury, and multi-organ dysfunction are among the other complications leading to death . several prognostic factors such as older age, male gender, presence of comorbidities and smoking have been found to be associated with severe disease or death zheng et al. 2020 ). in addition, deceased patients were more likely to have leukocytosis, lymphopenia and higher levels of lactate dehydrogenase, c-reactive protein (crp) , elevated neutrophil-tolymphocyte ratio , interleukin (il)-6 (aziz et al. 2020), troponin and d-dimer ). turkey has a comprehensive public healthcare system and all residents have received medical treatment free of charge in public and private hospitals during the covid-19 outbreak. according to the health ministry guideline, any suspected case who is over 50 years old or has any comorbidity should be hospitalized irrespective of vital signs, laboratory results and computed tomography (ct) findings (bilim kurulu, 2020) thus, a large proportion of patients with covid-19 meet criteria for admission as an inpatient. that might lead to over-hospitalization, resulting in many problems such as psychological disturbances, lack of sleep and accidental falls (zuk et al. 2003 , hitcho et al. 2004 the curb-65 and pneumonia severity index (psi) are widely used in predicting 30-day mortality in community acquired pneumonia (shah et al. 2010) . the curb-65 has been also found to be j o u r n a l p r e -p r o o f useful to predict 14-day mortality in hospital-acquired pneumonia (oktariani et al. 2019 ). however, they have not been studied in patients with covid-19. a simple predictive tool would be useful to estimate the risk of 30-day mortality and to stratify patients with covid-19 to high or low risk for poor outcome at the time of hospital admission. in this study, we aimed to assess whether curb-65 or psi is useful tool to predict 30-day mortality and to identify other factors that are associated with higher mortality in patients with covid-19. we performed a retrospective cohort study at gaziosmanpasa research and training hospital, university of health sciences, istanbul, turkey. our hospital has been working as a pandemic hospital since the outbreak began. our study was conducted in line with the declaration of helsinki. the local institutional ethics committee approved the study protocol (ethics approval number: 59/05.2020) and the requirement for written informed consent was waived by our ethics committee. the first case was reported on march 11, 2020 in turkey. management strategies have been revised and updated during the outbreak. as favipiravir treatment has become a suggested therapeutic option for covid-19 patients with severe pneumonia on april 2, 2020, we retrospectively enrolled the patients who have been diagnosed with covid-19 pneumonia at our center between april 2, 2020 and may 1, 2020. all patients over 18 years old with covid-19 confirmed by pcr on nasopharyngeal swab who were hospitalized in our hospital were included in the study. pregnant patients were excluded. based on the health ministry guideline, any suspected case who was over 50 years old, or had any comorbidity including cardiopulmonary disease, diabetes mellitus, hypertension, chronic renal disease, immunosuppressive conditions or malignancy, or with tachycardia (pulse >125/min), tachypnea (respiratory rate >22/min), hypotension (<90/60 mm hg) or hypoxemia (spo2 <93%) have been hospitalized. (bilim kurulu, 2020) severe cases were defined as those with any of the followings; (1) respiratory distress (>30 breaths/min), (2) oxygen saturation lower than <90% at rest, or (3) arterial partial pressure of oxygen/fraction of inspired oxygen ≦300mmhg (bilim kurulu, 2020). demographic characteristics, comorbidities, presenting symptoms, triage vitals including fever, blood pressure, respiratory rate, oxygen saturation at rest, heart rate, and initial laboratory parameters and time to death were collected from electronic medical records. our primary outcome was 30-day mortality defined as documented death from any cause during hospitalization or within 30 days of admission to our emergency department. the curb-65 and psi scores at hospital admission were calculated as shown in table 1 and table 2 . the curb-65 scores range from 0 to 4. having 0-1 scores indicate a low risk for mortality whereas 2 or higher scores are associated with higher mortality ( table 1 ). the psi scores are classified as group i, ii, iii, iv and v. patients are stratified into two levels of risk groups: psi low risk (group i-iii) and high risk (group iv-v) ( table 2) . protocol issued by the turkish ministry of health (bilim kurulu, 2020). the recommended j o u r n a l p r e -p r o o f hydroxychloroquine regimen for all hospitalized patients was a loading dose of 400 mg twice on day 1, followed by 400 mg daily for 4 additional days. in addition, azithromycin at a dose of 500 mg on day 1 and then 250 mg daily for 4 more was also used cautiously with qt interval monitoring. favipiravir was initiated in patients with severe pneumonia or in those with ongoing fever despite hydroxychloroquine and/or azithromycin treatment at a loading dose of 1600 mg twice on day 1, followed by 600 mg twice a day for 4 additional days. tocilizumab was used at a dose of 8mg/kg in patients with elevated inflammatory markers and ongoing hypoxemia despite favipiravir treatment. in case of inadequate clinical response, a second dose of tocilizumab was considered within 24-48 hours after the initial dose. prophylactic dose of enoxaparin has been initiated in all patients unless there was a contraindication. therapeutic dose of enoxaparin was used in the following conditions; severe pneumonia, d-dimer level  1000 ng/ml, body mass index  40 kg/m 2 , and acute venous thromboembolism. we used descriptive statistics to define variables. categorical data were reported as proportions and counts and continuous data were presented as median and interquartile range (iqr) unless the data were normally distributed. the sensitivity, specificity, and positive predictive value (ppv) and negative predictive value (npv) of curb-65  2 and psi  4 were calculated by the standard two-by-two tables. univariate and multivariate logistic regression analyses were performed to identify other independent predictors of 30-day mortality. the variables that are components of the curb-65 and psi as well as curb-65 and psi themselves were not taken into account in multivariate analysis. we used multiple logistic regression analysis to determine whether the curb-65, psi, and/or other independent risk factors predicted 30-day mortality. the discrimination capability of the combination of each prognostic scoring system with other factors j o u r n a l p r e -p r o o f was evaluated in the receiver-operating-characteristic analysis. the areas under the curves (auc) of the prediction models were compared using the delong and clarke-pearson approach (delong et al. 1988 ). p value < 0.05 was accepted as statistically significant. the analyses were computed with ibm spss statistics 23. a total of 681 patients were included in the study. mean ± sd age was 56.9 ± 15.7 years and 49% of the patients were female. three hundred and seventy (54.3%) patients had at least one comorbidity. the most common comorbidity was hypertension, followed by diabetes mellitus, asthma, chronic obstructive lung disease, ischemic heart disease, hyperlipidemia, chronic renal disease and congestive heart failure. the most common clinical presentations were fever (32.5%) and respiratory tract symptoms including cough (71.2%) and dyspnea (27.3%) ( table 3) . among the 681 patients hospitalized with covid-19, 672 (98.6%) patients had been initially transferred to the ward. of these, 596 (88.6%) patients were discharged, 74 (11%) patients were transferred to intensive care unit (icu), and 2 patients died in the ward. among the 74 patients transferred to icu, 45 patients died and 29 patients were discharged. among the 9 patients who were initially transferred to icu, 8 patients died and 1 patient was discharged ( figure 1 ). overall, 55 (8%) patients died within 30 days of admission to the hospital and the median time from admission to death was 9.5 (iqr: 6-22) days. deceased patients were older, more hypoxic, tachycardic, tachypneic and hypotensive at admission. they were more likely to have at least one comorbidity. regarding laboratory parameters, they had higher levels of neutrophil count, blood urea nitrogen, ferritin, crp, troponin and lower levels of lymphocyte count (table 3) . j o u r n a l p r e -p r o o f a total of 550 (80.8%) patients had a curb-65 score of 0 or 1. of these, 15 (2.7%) patients died within 30 days. one hundred thirty-one patients (19.2%) had a curb-65 score of ≥2. of these, 40 patients (30.5%) died within 30 days. a curb-65 score of ≥ 2 had a fair discriminatory ability to predict 30-day mortality with a sensitivity of 73%, specificity of 85%, ppv of 31%, npv of 97% (auc: 0.79, 95% ci 72 to 86, p <0.001) ( table 4 ). one hundred eighty-two patients (26.7%) were in group i, 249 patients (36.6%) were in group ii, 136 patients (20%) were in group iii, 82 patients (12%) were in group iv and 31 patients (4.7%) were in group v. there were no deaths among the patients in group i. the mortality rate was 2% in group ii, 4.4% in group iii, 28% in group iv, and 65.6% in group v. the psi group ≥ 4 had a good discriminatory ability to predict 30-day mortality with a sensitivity of 80%, specificity of 89%, ppv of 39%, npv of 98% (auc=0.85, 95% ci 78 to 90, p <0.001) ( table 4) . the univariate analysis revealed that levels of ferritin, crp, troponin and lymphocyte count were associated with 30-day mortality. after multivariate analysis, only elevated crp values (or:1.015, 95% ci 1.008 to 1.021, p<0.001) were significantly associated with 30-day mortality. (table 4) . aucs for 30-day mortality prediction of the curb-65 alone, psi alone and psi with crp were 0.88 with %95 ci from 0.85 to 0.90 (p <0.001), 0.91 with 95% ci from 0.88 to 0.93 (p <0.001) and 0.92 with 95% from 0.89 to 0.94 (p <0.001), respectively (figure 2 ). comparing the aucs for 30-day mortality prediction of the curb-65 alone, psi alone and the model including psi and crp levels showed that the two-variable model and psi alone predicted 30-day mortality significantly better than the curb-65 alone (p=0.01, p=0.04, respectively). however, j o u r n a l p r e -p r o o f discriminatory abilities of the psi and the two variable model including psi and crp were similar (p=0.29). in this study, we assessed the abilities of two prognostic scoring systems to predict 30-day mortality and evaluated independent predictive factors of mortality in a large group of patients with covid-19. the 30-day mortality rate was 8% in our study. the psi group ≥ 4 showed better sensitivity (80% vs 73%) and specificity (89% vs 85%) but a similar negative predictive value (98% and 97%) in predicting death compared to the curb-65 score of ≥ 2. only elevated levels of crp were independently associated with 30-day mortality. the psi scores alone and the twovariable model including psi scores and crp levels performed better than the curb-65 scores whereas the psi scores alone and the two-variable model had similar discriminatory ability in predicting 30-day mortality. the mortality rate of covid-19 has been reported as between 11.7% and 28.2%. cao et al. 2020; wu et al. 2019; giacomelli et al. 2020; huang et al. 2019) . the variation in the mortality rate may be due to the heterogeneity in the patient characteristics, treatment strategies and mortality measures (e.g. in-hospital or 30-day measure). in this study, our mortality rate was somewhat lower than reported in previous studies although our cohort had similar demographic features and comorbidities compared with previous studies cao et al. 2020; wu et al. 2019; giacomelli et al. 2020; huang et al. 2019; ) . the hospitalization criteria in turkey may be a possible explanation for this finding. as we mentioned earlier in introduction, a considerable number of non-severe patients were hospitalized according to their older age and/or coexisting comorbidities. thus, our cohort j o u r n a l p r e -p r o o f might represent less severe covid-19 patients. for instance, the proportion of severe cases at admission was 21.1% in our cohort while this was 63% in the study by zhou et al., and their mortality was 28% ). on the other hand, a retrospective study including only nonsevere cases at admission showed that 20 (5%) of the 348 patients became severe during hospitalization and 40% of them received only conventional oxygen therapy (duan et al. 2020 ). there have been ongoing attempts to develop a prognostic scoring system that can predict a poor outcome for patients with covid-19 (wynants et al. 2020) . the curb-65 scores were found to be significantly higher in deceased patients with covid-19 ). liu and colleagues compared the clinical characteristics and outcomes of elderly and young patients with and showed that the psi scores are higher in the elderly compared to young patients . as far as we know, this is the first study to evaluate the performance of the curb-65 and psi in the prediction of mortality. in our study, in predicting 30-day mortality, curb-65 score of ≥ 2 had a sensitivity of 73% and specificity of 85%, and psi group ≥4 had a sensitivity of 80% and specificity of 89%. when we analyzed the prognostic scoring systems as continuous variables, we found that psi scores alone predicted mortality significantly better than curb-65 scores (p=0.04). finally, we included crp levels to psi scale in order to improve its performance, however, adding crp levels to psi scale did not perform better than psi scores alone. a better discriminatory ability of psi scale was an expected finding since the psi scale consists of several parameters such as age, comorbidities, hypoxemia that were found to be associated with increased risk of mortality in patients with covid-19. more surprising was the finding that crp levels did not add prognostic information beyond psi scores alone. however, adding crp to psi scale also did not increase the prognostic performance of psi in hospitalized patients with communityacquired pneumonia (lee et al. 2011 ). since our first aim was to assess the performance of two prognostic scoring systems and to find additional variables that could improve their performance, we did not include variables that are components of these tools in the multivariate analysis. non-survivor patients had increased levels of crp, troponin, ferritin, lower lymphocyte counts and higher neutrophil counts compared to survivor patients. after multivariate analysis, elevated crp levels were significantly associated with increased risk for mortality and this finding was consistent with the previous studies. elevated crp levels were also reported to predict progression to severe illness and to correlate with the radiological extent of disease (duan et al. 2020; wang et al. 2020) . our study has some limitations. first, we did not calculate the prognostic scores prospectively. however, the hospitals in turkey has collected the clinical data in a standard format during the outbreak. regarding laboratory results, other than d-dimer levels there was no missing data as all the laboratory parameters were part of the routine evaluation of all hospitalized patients. second, among the previously reported risk factors for mortality in covid-19, our analysis did not take into account the potential risk factors such as body mass index, il-6 levels and radiological findings. in conclusion, this single center retrospective study including a large cohort of covid-19 patients showed that psi is a powerful tool to predict mortality in patients with covid-19. it performed significantly better than curb-65 and the addition of crp levels to psi scale did not improve the performance of psi. during the outbreak, psi can help physicians to stratify patients at admission. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. table 3 . comparison of demographic, clinical and laboratory findings between alive and deceased patients table 4 . discriminative accuracy of the curb-65 and psi in predicting 30-day mortality j o u r n a l p r e -p r o o f clinical features and short-term outcomes of 102 patients with corona virus disease comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach predictors of mortality for patients with covid-19 pneumonia caused by sarscov-2: a prospective cohort study correlation between the variables collected at admission and progression to severe cases during hospitalization among covid-19 patients in chongqing 30-day mortality in patients hospitalized with covid-19 during the first wave of the italian epidemic: a prospective cohort study characteristics and circumstances of falls in a hospital setting: a prospective analysis clinical features of patients infected with 2019 novel coronavirus in wuhan albumin and c-reactive protein have prognostic significance in patients with community-acquired pneumonia clinical features of covid-19 in elderly patients: a comparison with young and middle-aged patients clinical characteristics of novel coronavirus cases in tertiary hospitals in hubei province neutrophil-to-lymphocyte ratio as an independent risk factor for mortality in hospitalized patients with covid-19 curb 65 score as a predictor of early mortality in hospital-acquired pneumonia clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan validity of pneumonia severity index and curb-65 severity scoring systems in community acquired pneumonia in an indian setting c-reactive protein levels in the early stage of covid-19 who novel coronavirus (2019-ncov) situation report risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease prediction models for diagnosis and prognosis of covid-19 infection: systematic review and critical appraisal an interpretable mortality prediction model for covid-19 patients analysis of 92 deceased patients with covid-19 d-dimer levels on admission to predict inhospital mortality in patients with covid-19 risk factors of critical & mortal covid-19 cases: a systematic literature review and meta-analysis clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study essential psychological problems of hospitalized patients ii or iii versus iv or v. abbreviations: ci: confidence interval, ppv: positive predictive values, npv: negative predictive values, auc: area under curve key: cord-303417-1237ykxt authors: d’arminio monforte, antonella; tavelli, alessandro; bai, francesca; marchetti, giulia; cozzi-lepri, alessandro title: effectiveness of hydroxychloroquine in covid-19 disease: a done and dusted situation? date: 2020-07-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.056 sha: doc_id: 303417 cord_uid: 1237ykxt nan this is a pdf file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. this version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. arshad et al show evidence for a reduced mortality in covid-19 patients taking hydroxychloroquine alone or with azithromycin in an observational study in usa [1] . data on effectiveness and toxicity of hydroxychloroquine are controversial [2] [3] [4] [5] [6] . a total of 539 covid-19 hospitalised patients were included in our cohort in milan, from february 24 to may 17,2020 of whom 174 died in hospital (day 14 probability of death: 29.5% -95%ci: 25.5-34.0). we divided a subset of our cohort in three groups who started treatment a median of 1 day after admission: those receiving hydroxycholoroquine alone (n=197), those receiving hydroxycholoroquine+azithromycin (n=94), and those receiving neither (controls) (n=92). of the latter group, 10 started hiv antivirals (boosted-lopinavir or -darunavir), 1 teicoplanin, 12 immunomodulatory drugs or corticosteroids, 23 heparin and 46 remained untreated. the percent of death in the 3 groups was 27%, 23% and 51%. mechanical ventilation was used in 4.3% of hydoxychloroquine, 14.2% of hydroxycholoroquine+azithromycin and 26.1% of controls. unweighted and weighted relative hazards of mortality are shown in table 1 . after adjusting for a number of key confounders (see table) , the use of hydroxycholoroquine+azithromycin was associated with a 66% reduction in risk of death as compared to controls; the analysis also suggested a larger effectiveness of hydroxychloroquine in patients with less severe covid-19 disease (po2/fio2>300, interaction p-value<.0001). our results are remarkably similar to those shown by arshad et al. some important weaknesses of the analysis by arshad have been pointed out [7] but not all of these apply to our study. our propensity scores include some of the potential confounders that were missing in the analysis by arshad (e.g. calendar day of admission, disease severity, cardio-vascular disease (cvd), baseline plasma crp); second, we have excluded people receiving other drugs which could have biased the effect of hydroxychloroquine when used in combination. third, although residual confounding is a possibility (e.g. people with cvd were more frequent in control), people in the control group were more likely to undergo mechanical ventilation that is a conservative bias. these results from two different real-life settings (italy and usa), are conflicting with those of two large randomised trials [8, 9] . although unmeasured confounding remains the most likely explanation for the discrepancies, a robust meta-analysis is still lacking and we question whether hydroxychloroquine should be further tested. when best to start treatment is also a question that needs to be addressed in ad-hoc randomised studies. j o u r n a l p r e -p r o o f treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalised with covid-19 hydroxycholoroquine, a less toxic derivative of chloroquine, is effective in inhibiting sars-cov-2 infection in vitro hydroxychloroquine and azithromycin as a treatment of covid-19: results of an open-label non-randomised clinical trial hydroxychloroquine in patients mainly with mild to moderate covid-19: an open-label, randomised, controlled trial an observational cohort study of hydroxychloroquine and azithromycin for covid-19: (can't get no) satisfaction effect of desamethasone in hospitalized patients with cvid-19: preliminary report. covid-19 sars-cov-2 preprints from medrxiv and biorxiv 9-world health organization key: cord-292092-o6s5nw49 authors: furuse, yuki; okamoto, michiko; oshitani, hitoshi title: conservation of nucleotide sequences for molecular diagnosis of middle east respiratory syndrome coronavirus, 2015 date: 2015-09-30 journal: int j infect dis doi: 10.1016/j.ijid.2015.09.018 sha: doc_id: 292092 cord_uid: o6s5nw49 infection due to the middle east respiratory syndrome coronavirus (mers-cov) is widespread. the present study was performed to assess the protocols used for the molecular diagnosis of mers-cov by analyzing the nucleotide sequences of viruses detected between 2012 and 2015, including sequences from the large outbreak in eastern asia in 2015. although the diagnostic protocols were established only 2 years ago, mismatches between the sequences of primers/probes and viruses were found for several of the assays. such mismatches could lead to a lower sensitivity of the assay, thereby leading to false-negative diagnosis. a slight modification in the primer design is suggested. protocols for the molecular diagnosis of viral infections should be reviewed regularly after they are established, particularly for viruses that pose a great threat to public health such as mers-cov. middle east respiratory syndrome coronavirus (mers-cov) is an enveloped virus with a positive-sense rna genome. infection with the virus causes severe respiratory symptoms in humans, with a case fatality rate as high as 37%. 1 camels may be a source of infection to humans. 2 human-to-human transmission is also possible, but this requires close contact, such as health care-related contact without proper measures for infection control and prevention. 3 the earliest case of mers was reported in jordan, and mers-cov was subsequently isolated from cases in saudi arabia only a short time later. 4 since then, infections have been endemic mainly in the middle east. however, mers-cov has spread sporadically to other areas, including europe, north america, africa, and southeast and east asia, by travelers from the middle east. 5 the laboratory diagnosis of mers-cov infection is mainly performed using real-time reverse transcription pcr (rt-pcr) to detect viral rna in specimens. interim recommendations from the world health organization (who) in 2015 for the laboratory testing of mers-cov included protocols for rt-pcr that were developed by the university hospital bonn and the us centers for disease control and prevention. [6] [7] [8] [9] this document included seven assays: (1) the upe assay, which is considered highly sensitive and is recommended for screening, 7 (2) the orf1a assay, which is considered equally as sensitive as the upe assay, 6 (3) the orf1b assay, which is considered less sensitive than the orf1a assay, 6, 7 and the (4) n2 and (5) n3 assays, which can complement upe and orf1a assays for screening and confirmation. 8, 9 to date, these assays have shown no cross-reactivity with other human coronaviruses. [6] [7] [8] sequencing protocols for further confirmation, namely the (6) rdrpseq and (7) nseq assays, were also developed. 6 because mers-cov is an rna virus that can evolve rapidly, there remains concern that these protocols may not be suitable for the detection of current mers-cov because of a mismatch among sequences in the primer/probe regions. this study was performed to analyze recent viral genomic nucleic acid sequences and to discuss the efficacy of the rt-pcr protocols for the molecular diagnosis of mers-cov infections. 1 data for these 386 sequences, including complete as well as partial genome sequences, were obtained and analyzed. sequence data were aligned with clustalw to assess genetic changes in the nucleotide sequences of the primer and probe regions of the assays described above. the numbers of viral sequences that matched the primer/ probe sequences perfectly were counted. as mentioned in the introduction above, the upe, orf1a, n2, and n3 assays can be used for screening because of their high sensitivity. [6] [7] [8] [9] among these, only the primer and probe designs of the orf1a assay showed 100% conservation of all sequence data available today (table 1) . minor mismatches were found for the upe assay (one nucleotide substitution in two sequences) and n2 assay (one nucleotide substitution in one sequence), and significant mismatches were found for the n3 assay. the primer/probe regions were found to be well conserved, except for the n3 assay. in addition, mismatches were not found in the 3 0 end region of primers for the upe and n2 assays ( table 1 ). the sensitivity of the assays may not be greatly affected. no mismatches were found for the orf1b assay. with regard to the sequencing assays, no sequence data that matched the sequence of the reverse primer for the rdrpseq assay was found. however, a single common mismatch in all sequence data was found. when the mismatched nucleotide was corrected, the rdrpseq assay matched all the sequence data perfectly ('corrected reverse primer', table 1 ). in addition, viral sequences of the reverse primer region for the nseq assay were not highly conserved; the sequence matched only 49% of strains. based on these results, the use of a modified reverse primer for the assay is suggested, in order to reduce the possibility of a mismatch ('modified reverse primer', table 1 ). several mismatches among viral sequences in the primer/probe regions for molecular diagnosis were identified in this study. such mismatches could lead to a lower sensitivity of the assay, thereby leading to false-negative diagnosis. the mismatched sequence data could have been generated by errors in pcr or sequencing during viral nucleotide sequence analysis because of the incorporation of the wrong nucleotide. 10 however, it is more likely that the rna virus has evolved and that this has accidentally resulted in the induction of mutation/s in the region targeted by the primer/probe for rt-pcr, only 2 years after the establishment of the protocols. fortunately, no or few mismatches were found for most of the mers-cov screening assays. nevertheless, protocols for the molecular diagnosis of viral infections should be reviewed regularly after they are established, particularly for viruses that pose a great threat to public health such as mers-cov. middle east respiratory syndrome coronavirus (mers-cov) evidence for camel-to-human transmission of mers coronavirus first cases of middle east respiratory syndrome coronavirus (mers-cov) infections in france, investigations and implications for the prevention of human-to-human transmission isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome coronavirus (mers-cov): situation update and cases reported in the netherlands. who assays for laboratory confirmation of novel human coronavirus (hcov-emc) infections detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction real-time reverse transcription-pcr assay panel for middle east respiratory syndrome coronavirus world health organization. laboratory testing for middle east respiratory syndrome coronavirus-interim guidance (revised). who fidelity of dna polymerases in dna amplification this research was supported by the japan initiative for global research network on infectious diseases (j-grid) from the japan agency for medical research and development, amed. the funding source had no involvement in the study design, in the collection, analysis, and interpretation of the data, in the writing of the manuscript, or in the decision to submit the manuscript for publication.conflict of interest: all authors declare no conflicts of interest. table 1 conservation of the primer and probe region sequences of the who-recommended assays for the molecular diagnosis of mers-cov key: cord-282421-yialyuav authors: alcoba-florez, julia; gil-campesino, helena; de artola, diego garcía-martínez; gonzález-montelongo, rafaela; valenzuela-fernández, agustín; ciuffreda, laura; flores, carlos title: sensitivity of different rt-qpcr solutions for sars-cov-2 detection date: 2020-08-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.058 sha: doc_id: 282421 cord_uid: yialyuav abstract objectives the ongoing covid-19 pandemic continues imposing a demand for diagnostic screening. in anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative pcr (rt-qpcr) solutions to detect sars-cov-2. methods we evaluated six different rt-qpcr alternatives for sars-cov-2/covid-19 diagnosis based on standard rna extractions. that of best sensitivity was also assessed with direct nasopharyngeal swab viral transmission medium (vtm) heating, overcoming the rna extraction step. results we found a wide variability in the sensitivity of rt-qpcr solutions that associated with a range of false negatives from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). direct preheating of vtm combined with the best solution provided a sensitivity of 72.5% (62.5-81.0), in the range of some of the solutions based on standard rna extractions. conclusions we evidenced sensitivity limitations of currently used rt-qpcr solutions. our results will help to calibrate the impact of false negative diagnoses of covid-19, and to detect and control new sars-cov-2 outbreaks and community transmissions. . given the high sensitivity compared to serological testing (cassaniti et al. 2020) , standard diagnosis continues to rely on rna extractions from respiratory or oral samples followed by one-step reverse transcription and real-time quantitative pcr (rt-qpcr) that entail one or several primer-probe sets for targeting sars-cov-2 sequences . while it has been shown that protocol modifications aiming to overcome supply chain issues and accelerate diagnosis affect assay sensitivity (alcoba-florez et al. 2020; esbin et al. 2020) , differences in target priming efficiencies and rt-qpcr kit components are also expected to account for dissimilarities in false negative results (nalla et al. 2020 ). here we aimed to evaluate the sensitivity of six different rt-qpcr solutions, including five marketed kits and one based on the world health organization diagnostic assays with the best sensitivity vogels et al. 2020) , using rna extractions from nasopharyngeal swab viral transmission medium (vtm). the alternative with the best sensitivity was also assessed by a direct preheating of vtm samples to skip the rna extraction step that was described elsewhere (alcoba-florez et al. 2020). the study was conducted at the university hospital nuestra señora de candelaria (santa cruz de tenerife, spain) from march to june 2020. we evaluated six different rt-qpcr solutions ( table 1) , four based on three viral targets and two based on one viral target. since all samples were covid-19 positive for at least one solution/viral target, results with threshold cycle (ct) values above 40 or those that remained undetected during the 45 cycles of the experiments were considered fn observations (figure 1, table 1 ). attending to individual targets, we found that the most sensitive solution was the table 1 ). rt-qpcr for selected target genes of sars-cov-2 has been key in the global response to the pandemic. given the rapid spread of the virus at this time, it is likely that the rt-qpcr assays will continue to be a central tool for controlling covid-19. however, as happened in the past due to supply chain issues, policy decisions and laboratory testing capacities (alcoba-florez et al. 2020) , it is predictable that the diagnosis of covid-19 will continue relying on a variety of solutions among laboratories and countries (vogels et al. 2020) . our results evidenced a wide variability in the sensitivity of rt-qpcr solutions for sars-cov-2 detection which associated with a proportion of fn ranging from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). given that the same patient nasopharyngeal samples were assayed for the different solutions, well-known factors affecting sars-cov-2 sensitivity (stage of infection and type of specimen) (pan et al. j o u r n a l p r e -p r o o f 2020; wölfel et al. 2020) were suitably controlled in the study since all solutions were equally affected. thus, we are confident that the differences in sensitivity among solutions were due to their different components (i.e. primers-sets, buffers, enzymes and reagent contents in general). these findings will help to assess the impact of the selected solution on fn diagnoses of covid-19 (ramdas et al. 2020) and to choose a solution that minimize misdiagnoses of an active sars-cov-2 infection. jaf and cf designed the study. jaf, hgc, and dgm participated in data acquisition. jaf, lc and cf performed the analyses and data interpretation. lc, avf, rgm and cf wrote the draft of the manuscript. all authors contributed in the critical revision and final approval of the manuscript. corman et al. (2020) . fast sars-cov-2 detection by rt-qpcr in preheated nasopharyngeal swab samples members of the san matteo pavia covid-19 task force. performance of vivadiag covid-19 igm/igg rapid test is inadequate for diagnosis of covid-19 in acute patients referring to emergency room department detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr overcoming the bottleneck to widespread testing: a rapid review of nucleic acid testing approaches for covid-19 detection comparative performance of sars-cov-2 detection assays using seven different primer-probe sets and one assay kit viral load of sars-cov-2 in clinical samples report from the american society for microbiology covid-19 international summit test, re-test, re-test': using inaccurate tests to greatly increase the accuracy of covid-19 testing analytical sensitivity and efficiency comparisons of sars-cov-2 qrt-pcr primer-probe sets virological assessment of hospitalized patients with covid-2019 we deeply acknowledge the university hospital nuestra señora de candelaria board of directors and the executive team for their strong support and assistance in accessing diverse resources used in the study. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. this research was funded by cabildo insular de tenerife [grant number key: cord-293942-n5ypkftc authors: takoi, hiroyuki; togashi, yuki; fujimori, daiki; kaizuka, haruki; otsuki, shunsuke; wada, takuya; takeuchi, yoshikazu; abe, shinji title: favipiravir-induced fever in coronavirus disease 2019: a report of two cases date: 2020-09-28 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1450 sha: doc_id: 293942 cord_uid: n5ypkftc favipiravir, an antiviral agent, is undergoing clinical trials for treating novel coronavirus disease 2019 (covid-19). we report two cases of covid-19 with favipiravir-induced fever. in both cases, pyrexia was observed following administration of favipiravir despite symptoms of covid-19 improving. no other cause for the fever was evident after careful physical examination and laboratory investigation. once favipiravir was discontinued, the fever subsided in both patients. to our knowledge, this is the first report of favipiravir-induced fever. hiroyuki takoi, phd department of respiratory medicine, tokyo medical university hospital 6-7-1 nishi-shinjuku, shinjuku-ku, tokyo, 160-0023, tokyo, japan taco155485@hotmail.com the coronavirus disease 2019 pandemic is one of the most significant public health crisis in recent history. a randomized clinical trial showed that treatment with remdesivir accelerated recovery in patients with severe covid-19 (wang et al., 2020) . therefore, this antiviral agent has become one of the standard therapies for covid-19. favipiravir, a promising antiviral agent, is undergoing clinical trials as an alternative drug for treating covid-19 (arab-zozani et al., 2020) in several countries, including china (chen et al., 2020) , iran, germany, and japan. drug-induced fever is difficult to diagnose in patients with febrile illnesses, especially if the j o u r n a l p r e -p r o o f drug is a novel drug for an emerging infectious disease such as covid-19. reporting such cases might contribute to the accurate diagnosis of future cases. we experienced two cases of favipiravir-induced fever in patients hospitalized with covid-19. here we report the cases. in april 2020, a 42-year-old man was admitted to hospital with covid-19, 13 days after the onset of symptoms. he was taking febuxostat for hyperuricemia. on admission, he was asymptomatic and did not require supplemental oxygen. chest computed tomography (ct) showed ground-glass opacity in both lungs. favipiravir was started on the day of admission. he received two doses of 1,800 mg on day 1 and 800 mg twice daily thereafter. his uric acid level became elevated, possibly as a side effect of favipiravir; therefore, benzbromarone was added to his treatment regimen. on day 12 of favipiravir treatment, his temperature rose to 38°c with blood eosinophilia (630 cells/μl), despite an improvement in his chest x-ray findings. his general condition was good except for the fever and relative bradycardia. favipiravir treatment was discontinued on day 14, and his temperature returned to normal the following day ( fig. 1) . his blood eosinophil count also returned to normal. benzbromarone was initially considered to be the causative agent of the fever; however, clinical improvement occurred before benzbromarone was discontinued. thus, he was diagnosed with favipiravir-induced j o u r n a l p r e -p r o o f fever. in august 2020, a 28-year-old woman with an unremarkable medical history was admitted 5 days after the onset of covid-19 symptoms. she had a fever of 39°c, and her chest ct revealed mild ground-glass opacity at the base of each lung. she did not require supplemental oxygen. favipiravir treatment was started on the day of admission. she received two doses of 1,800 mg on day 1 and 800 mg twice daily thereafter. her temperature returned to normal the following day; however, on the following day, her temperature rose to 39°c. physical examination, laboratory investigation, and bacteriological and radiological findings did not determine the cause of the fever. her respiratory symptoms improved but she experienced relative bradycardia. drug-induced fever was suspected and favipiravir was discontinued on day 10. she became afebrile the following day and was discharged on day 15 (fig. 2) . in contrast to case 1, she did not develop blood eosinophilia. to our knowledge, this is the first report of favipiravir-induced fever. favipiravir is used to treat influenza a subtype h1n1. it exhibits antiviral activity against other rna viruses and is thought to have an antiviral effect on severe acute respiratory syndrome coronavirus-2 (shiraki and daikoku, 2020) . it has been approved in japan for treating novel influenza virus diseases. in a case series of 11 patients, favipiravir in combination with nafamostat mesylate was found to have an antiviral effect in critically ill covid-19 patients (doi et al., 2020) . in both of our cases, a discrepancy was observed between the patients' clinical course and their fever, and no possible cause of pyrexia other than favipiravir was identified. a definition of drug fever is "a disorder characterized by fever coinciding with the administration of a drug and disappearing after the discontinuation of the drug, when no other cause for the fever is evident after a careful physical examination and laboratory investigation," with a period of 1.3 ± 1.1 days from discontinuation of the causative drug to pyretolysis (makowiak and lemaistre, 1987) . drug fever can be ruled out if pyretolysis is not confirmed within 72 h after the discontinuation of the drug (mourad et al., 2003) . a wide variety of drugs have been implicated in drug fever (patel and gallagher, 2010 ). favipiravir has not been previously reported to cause drug fever. this preliminary report may help differentiate paradoxical fever in patients receiving favipiravir therapy for covid-19. early accurate diagnosis may reduce not only inappropriate, potentially harmful, and expensive diagnostic and therapeutic interventions, but may also lead to unnecessary patient isolation, bed occupation, and effort of healthcare workers. j o u r n a l p r e -p r o o f the patient's fever subsided after discontinuation of favipiravir. the patient's fever subsided after discontinuation of favipiravir. favipiravir for treating patients with novel coronavirus (covid-19): protocol for a systematic review and meta-analysis of randomised clinical trials favipiravir versus arbidol for covid-19: a randomized clinical trial nafamostat mesylate treatment in combination with favipiravir for patients critically ill with covid-19: a case series drug fever: a critical appraisal of conventional concepts. an analysis of 51 episodes in two dallas hospitals and 97 episodes reported in the english literature a comprehensive evidence-based approach to fever of unknown origin drug fever favipiravir, an anti-influenza drug against life-threatening rna virus infections remdesivir in adults with severe covid-19: a randomised, double-blind, placebo-controlled, multicentre trial both patients have provided written informed consent for the publication of this report. the authors did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors for writing this report. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.j o u r n a l p r e -p r o o f key: cord-278406-n5e3a09i authors: macauley, precious; martin, alvaro; epelbaum, oleg title: corticosteroids in the treatment of severe covid-19 lung disease: the pulmonology perspective from the first united states epicenter date: 2020-08-21 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.051 sha: doc_id: 278406 cord_uid: n5e3a09i the sars-cov-2 pandemic has introduced the medical community to a lung disease heretofore unknown to most clinicians. in much of the discourse about covid-19 lung disease, the more familiar clinical entity of ards has been used as the guiding paradigm. reflecting on studies in ards, particularly that due to influenza, and on data from the sars-cov and mers epidemics, many authorities, including within the discipline of infectious diseases, were initially passionate in their opposition to the use of corticosteroids for lung involvement in covid-19. the voice of the pulmonology community—the community of lung experts—has continued to be among the quietest in this conversation. herein we offer our perspective as academic pulmonologists who encountered covid-19 in its first united states epicenter of new york city. we encourage a conceptual separation between early covid-19 lung involvement and ards. we draw on history with other immune cell-mediated lung diseases, on insights from the sars-cov experience, and on frontline observations in an attempt to allay the skepticism towards corticosteroids in covid-19 lung disease that is likely to persist even as favorable study results emerge. as the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) pandemic first swept across the globe in the first quarter of 2020, the management of the associated clinical entity termed coronavirus disease 2019 became the subject of institutional recommendations (massachusetts general hospital, 2020), societal guidelines (bhimarj et al, 2020), and position statements (russell et al, 2020) . because acute respiratory failure (arf) in covid-19 is triggered by a viral pathogen, it is understandable that the discussion of this potentially devastating illness has centered on its infectious disease and epidemiologic implications. however, as pulmonologists who treated severe covid-19 patients in the first united states epicenter of new york city, we believe that something important has been underemphasized in this discourse. at the "heart" of covid-19 is a lung disease, and a question that has still not been raised often enough is: what exactly is the nature of the lung disease caused by sars-cov-2? more specifically, when progression to lung involvement appears, what would one see under the microscope in a section of lung tissue? this hypothetical question is of utmost importance because frontline experience indicates that reversal of covid-19 lung disease and avoidance of prolonged invasive mechanical ventilation (imv) is pivotal. all too frequently, the features of lung involvement in severe covid-19 have been conflated with the acute respiratory distress syndrome (ards), a clinically defined entity intended to correspond to the histological lung injury pattern known as diffuse alveolar damage (dad). the correlation between ards and pathological dad is highly imperfect (thille et al, 2013) , and ards has a number of well-described mimics among diffuse lung diseases with acute presentations (schwarz et al 2004) . the importance of differentiating ards from its mimics is that, unlike dad, many histological patterns in the mimic category are exquisitely corticosteroid-sensitive. early in the pandemic, it was recognized that the physiological behavior of covid-19 lung disease is often j o u r n a l p r e -p r o o f distinct from that typically encountered in ards/dad (gattinoni et al, 2020) . to the trained eye of a pulmonologist, the thoracic imaging appearance of early covid-19 lung disease is less reminiscent of corticosteroid-resistant ards/dad and more reminiscent of corticosteroidsensitive substrates such as organizing pneumonia (op), acute eosinophilic pneumonia (aep), and vasculitis (hani et al, 2020; nemec et al 2013) . although both influenza and coronavirus infect respiratory epithelial cells, there is histopathological evidence from the 2003 severe acute respiratory syndrome coronavirus (sars-cov) epidemic to suggest that the former has a more dramatic propensity than the latter for catastrophic lung injury in the form of dad (ng et al, 2006 ). clinicoradiological differences between covid-19 lung disease and that of influenza are likewise emerging to support the histopathological observations (tang et al, 2020) . this is consistent with our clinical experience in covid-19. figure 1 depicts the chest radiographs (cxr) of three representative patients with covid-19 admitted to the intensive care unit (icu) of our institution; each row of the panel corresponds to a single patient. the cxrs on the left (panels a, c, e) were obtained on the day of icu admission while the cxrs on the right (panels b, d, f) were obtained less than 24 hours later. in each case, the only pharmacological intervention these patients received between the two cxrs that could account for a dramatic improvement in lung consolidation within such a short period of time is a single one gram "pulse" dose of methylprednisolone. this type of radiographic behavior is decidedly uncharacteristic of ards/dad but is quite characteristic of the corticosteroid-sensitive ards/dad mimics mentioned above. while caring for scores of severe covid-19 lung disease patients and repeatedly witnessing a striking clinicoradiographic response to pulse corticosteroids, we were disheartened by the initial negativity towards corticosteroids expressed by, among others, our infectious disease colleagues (massachusetts general hospital, 2020; the use of corticosteroids in pulmonary medicine, including at pulse dose, for certain diffuse lung diseases, a practice that is readily applied even to novel entities such as e-cigarette or vaping product-use associated lung injury (evali) that lack any evidence base (layden et al, 2020) . many of the studies labeled inconclusive were never intended to specifically examine the role of corticosteroids. if one restricts the view to just those english-language studies designed to investigate corticosteroid regimens, an overall optimistic picture emerges, particularly considering that the survival figures include critically ill patients (table 1 ) (fowler et al 2003) . the most discouraging study in this group is a retrospective analysis of critically ill mers patients showing a very high mortality with no survival advantage attributable to corticosteroids (arabi et al, 2018) . it is worth considering that corticosteroids were administered based on clinicians' discretion a median of three days into icu stay at a median dose in methylprednisolone equivalents of 60mg, very different from the one gram of methylprednisolone starting on the day of icu arrival and continued for three days that has been our practice with severe covid-19 lung disease. this study, along with another from the sars-cov era , implicated corticosteroids in persistence of viral rna. corticosteroid therapy for critically ill patients with middle east respiratory syndrome infectious disease society of america guidelines on the treatment and management of patients with covid-19 last accessed augustpril 118 early corticosteroids in severe influenza a/h1n1 pneumonia and acute respiratory distress syndrome treatment of severe acute respiratory syndrome with glucosteroids: the guangzhou experience early short course corticosteroids in hospitalized patients with covid-19 acute respiratory distress syndrome: advances in diagnosis and treatment critically ill patients with severe acute respiratory syndrome covid-19 does not lead to a "typical" acute respiratory distress syndrome osteonecrosis of hip and knee in patients with severe acute respiratory syndrome treated with steroids covid-19 pneumonia: a review of typical ct findings and differential diagnosis high-dose pulse versus nonpulse corticosteroid regimens in severe acute respiratory syndrome outcome of coronavirus-associated severe acute respiratory syndrome using a standard treatment protocol pulmonary illness related to e-cigarette use in illinois and wisconsin -final report factors associated with psychosis among patients with severe acute respiratory syndrome: a case-control study effects of early corticosteroid treatment on plasma sars-associated coronavirus rna concentrations in adult patients massachusetts general hospital covid-19 treatment guidance the general hospital corporation (us) covid-19: consider cytokine storm syndromes and immunosuppression noninfectious inflammatory lung disease: imaging considerations and clues to differential diagnosis the comparative pathology of severe acute respiratory syndrome and avian influenza a subtype h5n1-a review lung pathology of fatal severe acute respiratory syndrome radiologypathology correlation in recovered covid-19, demonstrating organizing pneumonia dexamethasone in hospitalized patients with covid-19 -preliminary report clinical evidence does not support corticosteroid treatment for 2019-ncov lung injury imitators" of the ards: implications for diagnosis and treatment sars: systematic review of treatment effects severe acute respiratory syndrome: report of treatment and outcome after a major outbreak comparison of hospitalized patients with ards caused by covid-19 and h1n1 comparison of the berlin definition for acute respiratory distress syndrome with autopsy pulmonary pathology of early-phase 2019 novel coronavirus (covid-19) pneumonia in two patients with lung cancer severe acute respiratory syndrome (sars) coronavirus-induced lung epithelial cytokines exacerbate sars pathogenesis by modulating intrinsic functions of monocyte-derived macrophages and dendritic cells corticosteroid treatment of patients with coronavirus disease 2019 (covid-19) histopathologic changes and sars-cov-2 immunostaining in the lung of a patient with covid-19 this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. this manuscript preparation did not require ethical approval. none acknowledgements none key: cord-276445-m5vjo3ym authors: lee, hyojung; nishiura, hiroshi title: recrudescence of ebola virus disease outbreak in west africa, 2014–2016 date: 2017-09-20 journal: int j infect dis doi: 10.1016/j.ijid.2017.09.013 sha: doc_id: 276445 cord_uid: m5vjo3ym objectives: there have been errors in determining the end of the ebola virus disease (evd) epidemic when adhering to the criteria of the world health organization. the present study aimed to review and learn from all known recrudescence events in west africa occurring in 2014–2016. methods: background mechanisms of five erroneous declarations in guinea, liberia, and sierra leone during 2014–2016 were reviewed. results: three cases of recrudescence were suspected to have been caused by sexual contact with survivors, one to be due to international migration, and one was linked to a potentially immunocompromised mother. the three sexual transmission events involving survivors—the first two in liberia and one in sierra leone—required 164 days, >150 days, and approximately 180 days, respectively, from discharge of the survivors to confirmation of the recrudescent case. conclusions: the events of recrudescence were associated with relatively uncommon routes of transmission other than close contact during burial or care-giving, including sexual transmission, possible immunocompromise, and migration. recognition of the sexual transmission risk among survivors could potentially involve discrimination, which may lead to under-ascertainment. the end of an outbreak must be determined objectively (nishiura et al., 2016) . for the ebola virus disease (evd) outbreak in west africa from 2014 to 2016, the world health organization (who) recommended securing 42 days (world health organization, 2015) , or twice the observed maximum incubation period, from the time at which the last case was found negative for the virus at second testing. subsequently, the country without evd cases would enter a period of heightened surveillance lasting 90 days to monitor for any other occurrence of infection. as there have been errors in determining the end of an outbreak when adhering to the criteria mentioned above, it would be valuable to learn from the events of evd recrudescence occurring in liberia, guinea, and sierra leone. this will inform wiser decision-making in the future. the present study aimed to review all known recrudescence events in west africa occurring during the period 2014-2016. a recrudescence event was defined as the reappearance of at least one confirmed case of evd in a country where the end of evd had been declared in advance. the term 'recrudescence' is used, because the reappearance of evd in west africa has been associated with persistent activity of infection arising from already infected humans. who reports and other sources were reviewed in an analysis of all known recrudescence events occurring from 2014 to 2016 (world health organization, 2016; sheri, 2015; farge and giahyue, 2015; dahl et al., 2016; dakaractu, 2016; center for infectious disease research and policy, 2016) . in the statistical analysis, the background mechanisms of erroneous declarations of the end of an evd outbreak in west africa during 2014-2016 were investigated. a survey of the demographic variables of recrudescent cases was performed (i.e., age and sex), and the most likely source of infection and the dates of illness onset and confirmation were also obtained. by examining the date of confirmation of the purported last case (i.e., the case before the recrudescent case) and the date on which the outbreak was declared to have ended, the following were calculated: (1) the time interval between successive confirmations, (2) the number of days from burial or the second negative testing result of the last case, and (3) the number of days in heightened surveillance. a total of five cases of recrudescence were identified ( figure 1 ): three occurred in liberia and one each in guinea and sierra leone (world health organization, 2016; sheri, 2015; farge and giahyue, 2015; dahl et al., 2016; dakaractu, 2016; center for infectious disease research and policy, 2016) . two were male and three were female ( table 1) . one of the three cases in liberia was caused by inter-country migration, and therefore may be better stated as recurrence rather than recrudescence (world health organization, 2016; dakaractu, 2016) . that case was associated with viral exposure at a funeral in guinea (dakaractu, 2016) . sexual transmission involving survivors was suspected for three cases (world health organization, 2016; sheri, 2015; center for infectious disease research and policy, 2016) . of these, one in liberia was documented as linked to a survivor who had recovered 164 days before confirmation of the recrudescent case (dahl et al., 2016) . similarly, the recrudescent female case in sierra leone is believed to have been due to sexual transmission (world health organization, 2016; center for infectious disease research and policy, 2016). in guinea, three probable unconfirmed deaths considered as consistent with evd were observed in advance of the confirmed recrudescence on march 17, 2016 (world health organization, 2016 dahl et al., 2016; dakaractu, 2016) . virologically, the causative virus of the recrudescence event was demonstrated to be closely related to the virus isolated previously in the same country (dahl et al., 2016; dakaractu, 2016) . the route of transmission in a 15-year-old male in liberia remains unknown, but intra-household transmission during the mother's pregnancy from the immunocompromised mother to the 15-year-old boy was suspected (world health organization, 2016; farge and giahyue, 2015) . the time interval from laboratory confirmation of the perceived last case to confirmation of the recrudescent case ranged from 101 to 140 days (table 1 ). all observed intervals were longer than the mean serial interval; i.e., the time from illness onset in the primary case to that in the secondary case, estimated at 15.3 days (who ebola response team, 2016) . from the latest date of either burial or second negative test result, it took 92-122 days to confirm the cases of recrudescenceall more than double the 42-day waiting period. recrudescence events occurred 51-79 days after the declaration of the end of the outbreak. the time lags from declaration to recrudescence were all within the 90-day period of heightened surveillance. the three sexual transmission events involving survivors-the first two in liberia and one in sierra leone-required 164 days, >150 days, and approximately 180 days, respectively, from discharge of survivors to confirmation of the recrudescent case. the recrudescence events were not associated with the common routes of evd transmission, such as close contact during burials or care-giving, but rather with other routes or reasons, including sexual transmission, possible immunocompromise, and migration. while use of a 42-day waiting period posed practical difficulties from 2014 to 2016, the present exercise was not intended to criticize that fixed, transparent criterion. even with the use of a more objective approach, including serial interval distribution (e.g., as applied for middle east respiratory syndrome in south korea (nishiura et al., 2016) ), this may not have sufficiently captured the involvement of sexual transmission and other reasons for recrudescence. the need to consider the prevention of sexual transmission via survivors when declaring the end of an epidemic poses a dilemma. this is because the recognition of such a risk among survivors could potentially involve discrimination, and fear of stigma may lead to under-ascertainment. the results of this study suggest that the supposed end of an evd epidemic could be divided objectively into several different types. for instance, the restriction of movement for cases and exposed individuals-i.e., socially 'costly' interventions-could be ceased through use of a 42-day waiting period. this may not necessarily ensure a long enough waiting time for an uncommon route of infection. meanwhile, heightened surveillance and the avoidance of risky sexual intercourse should be set at >180 days, i.e. the observed maximum in this study, echoing a study on the transmission network (mate et al., 2015) ; ideally this duration should be set at 9 months considering the persistence of the virus in semen (deen et al., 2015) . these are essential to monitor and prevent recrudescence through uncommon routes of transmission. it is intended to investigate the objective determination of the outbreak in a more explicit manner using mathematical modeling techniques. not applicable. sierra leone reports second new ebola case cdc's response to the 2014-2016 ebola epidemic -guinea related ebola cases in guinea and liberia ebola rna persistence in semen of ebola virus disease survivors -preliminary report female survivor may be cause of ebola flare-up in liberia. reuters molecular evidence of sexual transmission of ebola virus objective determination of end of mers outbreak surge of ebola in liberia may be linked to a survivor who ebola response team. after ebola in west africa -unpredictable risks, preventable epidemics criteria for declaring the end of the ebola outbreak in guinea, liberia or sierra leone. geneva: world health organization world health organization. ebola situation report. geneva: world health organization table 1 recrudescence of ebola virus disease in west africa hn received funding from the japan agency for medical research and development (amed), japanese society for the promotion of science (jsps) kakenhi (grant numbers 16kt0130, 16k15356, and 17h04701), japan science and technology agency (jst) crest program (jpmjcr1413), and ristex program for science of science, technology and innovation policy. hl has received financial support through the jsps program for advancing strategic international networks to accelerate the circulation of talented researchers. the funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. the authors declare no conflicts of interest. (2016) a duration from confirmation of the last case to confirmation of the re-emerging case. b duration from burial or the second negative testing result of the last case to confirmation of the re-emerging case. c a declaration was made on the day following the negative laboratory test and, thus, the specified date minus 42 does not equal 68 days, as in the next column to the right. key: cord-283812-ocfjj79v authors: blumberg, lucille; regmi, jetri; endricks, tina; mccloskey, brian; petersen, eskild; zumla, alimuddin; barbeschi, maurizio title: hosting of mass gathering sporting events during the 2013–2016 ebola virus outbreak in west africa: experience from three african countries date: 2016-06-15 journal: int j infect dis doi: 10.1016/j.ijid.2016.06.011 sha: doc_id: 283812 cord_uid: ocfjj79v • mass gatherings at sporting events attract millions of international and national host-country travellers, who may put themselves at risk of acquiring local endemic infectious diseases. • the 2013–2016 ebola virus disease (evd) outbreak in west africa that resulted in over 28 637 cases and 11 315 deaths required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of evd. • three major sports events were held in africa during the evd outbreak, attended by athletes from numerous african countries including liberia, sierra leone, and guinea, the three countries most affected by evd: the african youth games (botswana), africa cup of nations (equatorial guinea), and all-africa games (republic of congo). • a large range of infectious diseases other than evd were considered with respect to the differential diagnosis of acute febrile illnesses and for the provision of laboratory diagnostics and treatment options. • the experience from these three mass gathering events during the ebola epidemic illustrates that these events can be held safely provided that countries put measures in place for enhanced surveillance and response systems for communicable diseases. mass gatherings at sporting events, 1,2 or religious pilgrimages, 3, 4 attract millions of international and national hostcountry travellers, who put themselves at risk of acquiring local endemic infectious diseases. [5] [6] [7] over the past five decades, the public health authorities of the host country have focused their attention on the transmission of infectious diseases and their impact on the attendees at the mass gathering, the local population, and the local health system. the appearance and reemergence of several new lethal pathogens of humans with epidemic potential have heightened awareness of the potential of rapid spread at mass gathering events. 8 new zoonotic infectious diseases of humans include nipah virus, hantaviruses, west nile virus, ebola virus, severe acute respiratory syndrome coronavirus (sars-cov), middle east respiratory syndrome coronavirus (mers-cov), and avian viruses, among others. 7, 8 the unprecedented ebola virus disease (evd) epidemic in west africa 9 and the ongoing zika virus (zikv) outbreak in south america 10, 11 were declared public health emergencies of international concern (pheic) by the world health organization (who) in august 2014 and february 2016, respectively. yellow fever outbreaks in a number of african countries in 2015/2016 are cause for concern, with infections in unvaccinated travellers to angola posing a risk on return to their countries of residence. 12, 13 there are a number of challenges for countries hosting major international sporting events during a pheic. 4, 14, 15 the 2013-2016 evd outbreak in west africa, which resulted in over 28 637 cases and 11 315 deaths, 16 required that countries holding these events put in place public health programmes for enhanced surveillance and specific response plans for any suspected cases of viral haemorrhagic fever (vhf). three major sports events were held in africa during different phases of the ebola virus outbreak, with participation by sportsmen and women and supporters from a broad range of african countries, including liberia, sierra leone, and guinea, the three most affected countries. at the invitation of the host countries, who missions were conducted to the three respective countries to support and advise on specific ebola prevention and response strategies. in this article, the three major sporting events are described, highlighting the activities undertaken to ensure public health security and the outcomes of these mass gatherings with specific reference to evd. the african youth games are held every 4 years. the first games were hosted by morocco in rabat and 1000 athletes from 40 countries participated. the second african youth games were held in gaborone, the capital city of botswana, from may 22 to may 31, 2014; in retrospect, this was at a time when the ebola virus outbreak had expanded rapidly within the affected region. this event took place at a number of venues in gaborone and drew around 2000 athletes aged 15 to 20 years, who took part in a wide range of sporting events including football, swimming, fencing, boxing, cycling, and rugby, as well as their support teams; the participants came from 51 african countries including liberia, sierra leone, and guinea. spectator attendance was mainly from botswana and countries in the region. at the beginning of may 2014 the ministry of health of botswana was on high alert and requested that the who provide rapid technical support in strengthening public health capacities under the framework of the international health regulations (ihr) 2005, in the context of the expanding ebola virus outbreak. botswana had never previously managed cases of suspected or confirmed vhf. while no general travel restrictions were applied to athletes from the evd-affected countries, contacts of known cases of evd were not permitted to leave their respective countries. proof of yellow fever vaccination was required as a condition of entry for travellers from yellow fever endemic countries. at the international airport in gaborone, port health staff screened incoming travellers for fever; they were supported by a small team of medical personnel trained for the event. a small medical facility was established at the airport for the isolation of patients. while a strong national surveillance system supported by district outbreak response teams was already in place for epidemic-prone diseases, this was supplemented by a daily surveillance system for specific priority conditions pertinent to the event. both a syndromic approach and laboratory confirmation to identify participants with an acute febrile illness were used. a daily analysis attempted to establish trends. an emergency 24-h reporting system was established for persons with suspected meningitis or vhf, and for any outbreaks. an isolation facility was established in an existing health centre outside of the major hospitals. extensive staff training was conducted using videos and demonstrations in the use of personal protective equipment (ppe) and infection control practices, as well as simulation exercises. sourcing of adequate supplies of ppe was a challenge. since botswana did not have laboratory capacity for vhf and other specialized testing, arrangements were made for testing to be conducted in the biosafety level 4 (bsl4) laboratory and reference laboratories at the national institute for communicable diseases in south africa, approximately 4 h by road from gaborone. the requisite export permits and transport arrangements were facilitated. the public health and hospital laboratories in gaborone were able to test for malaria and meningitis and common pathogens. training sessions in the recognition and management of a range of communicable diseases were held for medical personnel. the 2015 africa cup of nations competition was organized by the confederation of african football and held in equatorial guinea between january 17 and february 8, 2015. initially scheduled to be hosted by morocco, this major football tournament was moved to equatorial guinea at a late stage after morocco requested postponement due to the ebola virus epidemic in west africa. south africa, egypt, ghana, and sudan all declined to take over as hosts. fifty-one countries competed and 16 qualified for the tournament: south africa, equatorial guinea, congo, mali, algeria, gabon, burkina faso, cameroon, cote d'ivoire, guinea, ghana, zambia, tunisia, senegal, democratic republic of congo, and cape verde. four cities in equatorial guinea hosted the event: the capital city malabo, bata, mongomo, and ebebiyin. in addition to supporting the overall evd preparedness, the main objective of the joint who team was to strengthen the country's readiness to detect and manage evd during the africa cup of nations. equatorial guinea had never previously detected a human case of evd, neither associated with the most recent epidemic in west africa nor during any previous outbreak. nevertheless, the neighbouring country of gabon verified its first evd outbreak in 1994 and detected sporadic evd outbreaks in 1996 and 2001/2002, with 124 confirmed cases and 97 deaths reported. 17 with people coming to the country from many african countries, the risk of importing evd existed and required mitigation. a crisis committee to coordinate preparedness and response activities for evd, chaired by the prime minister, was established in december 2014 following the declaration of the pheic by the who. overall, no major communicable disease events were reported. the republic of congo hosted the xi edition of the all-africa games. the games were held in 11 stadia throughout the city of brazzaville from september 4 to september 19, 2015, with participation of athletes from 54 countries, including sierra leone, liberia, and guinea. the ministry of health and population of congo was responsible for the overall coordination and delivery of health services, and worked in close collaboration with other ministries, the organizing committee, and the who, to ensure rapid detection and containment of infectious diseases, especially evd. the republic of congo had previous experience of managing vhf with referral to the reference laboratory in kinshasa, democratic republic of congo, directly across the congo river from brazzaville. health risks to visitors and local communities during the all-africa games were assessed at an early stage, and planning for constant disease surveillance and risk assessment during the event was organized. enhanced surveillance for key notifiable diseases was implemented in all 11 stadia and other important locations like the airport. during the games, the ministry of health participated in daily all-hazard assessment with the national organizing committee and developed and shared daily situation reports. the data gathered from the surveillance units at the sports village during the events showed that of the 731 cases reported from the sports sites during the events, trauma accounted for 43%, followed by malaria at 27% and respiratory tract infections at 15%. no significant threat to public health was detected during the event, with a minimum effect on the surge capacity of the public health services. thus, early planning, risk assessment, and preparedness activities as well cross-sectoral collaboration resulted in successful organization of the event amidst the ongoing evd in west africa. no major public health incidents occurred during the three major sporting events. each of the countries enhanced their surveillance and reporting systems. only a few outbreaks of gastrointestinal and respiratory infections and malaria and a few traumatic injuries were recorded during the period, and importantly, no suspected cases of evd or other vhf occurred. while outbreaks of infectious diseases have been reported during events, mostly from faeco-oral, respiratory, and vectorborne transmission, to date there have been no published incidents of a case of vhf presenting at a mass gathering. [4] [5] [6] even though the risk of introduction of a case of evd would in reality be quite low, the high profile of these sporting events and the major negative effect of even one suspected or confirmed case on the games, necessitated special preparations over and above those needed to monitor and manage the more usual communicable disease risks associated with mass gatherings. persons with early or acute evd are less likely to travel and unlikely to take part in a sporting event. exit screening was introduced after the declaration of evd as a pheic, and transmission requires direct contact with blood and body fluids of infected persons. 18 however, evd was spread to a number of countries through travel, 19 persons are asymptomatic during the incubation period, sexual transmission by survivors is now well documented, 20 and certain contact sports may pose a risk, albeit small, for transmission. with specific reference to evd, the challenges are the nonspecific nature of early illness with its broad differential diagnosis, the infrequent finding of haemorrhage, which could raise the index of suspicion of a vhf, the many other infections presenting with bleeding, delays in laboratory exclusion of vhf in the settings of these three events or the confirmation of alternative diseases, the need to ensure that patients receive adequate treatment for common infectious diseases and importantly for a mass gathering scenario, the potential for panic amongst athletes and the local communities, and the risk of potential disruption to the games. there are many additional resources needed to respond to potential vhf cases, some of which are not readily available, and these require additional funding. given the countries of origin of the participants and spectators, a large range of infectious diseases other than evd needed to be considered with respect to the differential diagnosis of acute febrile illness and the provision of laboratory diagnostics and treatment options. training of health workers and resources needed to be provided, given that these were not necessarily common diseases in the host countries. these conditions included trypanosomiasis, meningococcal disease, crimean-congo haemorrhagic fever (cchf), lassa fever, dengue, arboviral infections, and leptospirosis, as well as the more familiar typhoid, malaria, hepatitis (a, b, and e), hiv, sexually transmitted infections, tuberculosis, and gastrointestinal (viral and bacterial) and respiratory infections, including influenza. the annual influenza season in temperate zones in southern africa typically occurs from late may to august. meningococcaemia or meningococcal meningitis was a particular concern, given the increased risks in young people, particularly those in close contact in hostel-type accommodation, the origin of some of the participants from countries within the african meningitis belt, and possible increased carriage rates. the typically very rapid progression to severe illness over a matter of hours, difficulty in recognition because of nonspecific signs and symptoms, particularly with meningococcaemia, high mortality rates, and occurrence of bleeding with confusion with vhf, was particularly concerning in the setting of a mass gathering. overall, for vaccine preventable diseases, such as measles, meningococcal meningitis, pneumococcal sepsis, influenza, mumps, and hepatitis a, pre-travel vaccination for participants is known to reduce disease incidence at mass gatherings. meningococcal disease at the hajj has rarely been recorded since pre-travel vaccination was enforced. for communicable diseases that do not have vaccines available, a high state of public health alert, with public health teams on standby coupled to educating the attendees and local population, can go a long way in improving their prevention and detection. brazil will be hosting the 2016 olympics in rio de janeiro in august 2016, with many thousands of people from all over the world travelling to brazil. the unexplained rapid spread of the mosquito-borne zikv across south and central america adds another viral threat (in addition to dengue, japanese encephalitis, and yellow fever) for the attendees of the olympic games, further challenging preparedness and surveillance efforts. south africa successfully hosted two mass gatherings during the influenza a (h1n1)pdm09 virus pheic without any major communicable disease incidents. these were the confederation cup in 2009 and the fifa soccer world cup in 2010. while epidemics due to vector-borne transmission pose different challenges to ebola virus and influenza, the same principles of enhancing surveillance and response efforts and reducing all possible risks would apply. the experience garnered during these three mass gathering events during the ebola epidemic illustrates that these events can be held safely even during a pheic provided that countries put measures in place for enhanced surveillance for communicable diseases and are well prepared to respond to any incidents. although additional resources and training will be required, the efforts are worthwhile and form part of the legacy of mass gatherings for the detection and response to future cases or outbreaks of formidable diseases. european football championship finals: planning for a health legacy olympic and paralympic games: public health surveillance and epidemiology hajj: infectious disease surveillance and control global perspectives for prevention of infectious diseases associated with mass gatherings communicable diseases as health risks at mass gatherings other than hajj: what is the evidence? emerging infectious diseases and pandemic potential: status quo and reducing risk of global spread emerging respiratory tract viral infections emerging and re-emerging infectious threats in the 21st century world health organization. ebola virus diseases outbreak rapid spread of zika virus in the americas-implications for public health preparedness for mass gatherings at the 2016 brazil olympic games yellow fever cases in asia: primed for an epidemic why is the yellow fever outbreak in angola a 'threat to the entire world'? public health for mass gatherings mass gatherings and public health: the experience of athens 2004 olympic games. who/euro ebola virus disease outbreak, end of ebola transmission in guinea and liberia morbidity and mortality of wild animals in relation to outbreaks of ebola haemorrhagic fever in gabon transmissibility and pathogenicity of ebola virus: a systematic review and meta-analysis of household secondary attack rate and asymptomatic infection assessing the impact of travel restrictions on international spread of the 2014 west african ebola epidemic potential impact of sexual transmission on ebola virus epidemiology: sierra leone as a case study we thank the public health authorities of botswana, equatorial guinea, and the republic of congo and their respective who representatives.conflict of interest: the authors have no conflict of interest to declare. key: cord-292988-q1yz9y8k authors: zumla, alimuddin; wang, fu-sheng; ippolito, giuseppe; petrosillo, nicola; agrati, chiara; azhar, esam i; el-kafrawy, sherif a; osman, mohamed; zitvogel, laurence; locatelli, franco; gorman, ellen; o'kane, cecilia; mcauley, danny; maeurer, markus title: reducing mortality and morbidity in patients with severe covid-19 disease by advancing ongoing trials of mesenchymal stromal (stem) cell (msc) therapy achieving global consensus and visibility for cellular host-directed therapies date: 2020-05-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.040 sha: doc_id: 292988 cord_uid: q1yz9y8k abstract as of may 11th 2020, the coronavirus disease 2019 (covid-19) pandemic, caused by the novel, the severe acute respiratory syndrome coronavirus-2 (sars-cov-2) has caused 274,361 deaths out of 3,917,366 (7% case fatality rate). as with the two other novel coronavirus zoonotic diseases of humans, sars and mers, no specific treatments for reducing mortality or morbidity are yet available. deaths from covid-19 will continue to rise globally until effective and appropriate treatments and vaccines are found. with no specific treatments being available for treating covid-19 patients, the global medical, scientific, pharma and funding communities have rapidly initiated over 500 covid-19 clinical on a range of antiviral drug regimens, biologics, repurposed drugs in various combinations. we focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (stem) cells (mscs) in treatment trials of patients with severe covid-19 disease. this is an area which has been eclipsed by the current emphasis the huge number of trials evaluating new anti-viral drugs, repurposed drugs and combinations thereof. mscs should also be trialed for treatment of severe cases of mers where mortality rates are upto 34% and mers-cov remains a who priority blueprint pathogen. it’s about time funding agencies now invest more into development mscs per se and other host-directed therapies in combination with other therapeutic interventions. msc therapy could turn out to be an important contribution to bringing an end to the high covid-19 and mers death rates. caused by the novel, highly contagious zoonotic pathogen, the severe acute respiratory syndrome coronavirus-2 (sars-cov-2) (hui d et al, 2020) . by may 11 th 2020, there have been 274,361 deaths out of 3,917,366 (7% case fatality rate) confirmed covid-19 cases reported from all continents to the world health organization (who, 2020) . as with the two other novel coronavirus zoonotic diseases of humans, sars and mers, no specific treatments for reducing mortality or morbidity are yet available hui and zumla, 2020) . the management of covid-19 patients remains largely symptomatic and supportive with organ support for severely ill patients. deaths from covid-19 will continue to rise globally until effective and appropriate treatments and vaccines are found. with no specific treatments being available for treating covid-19 patients, the global medical, scientific, pharma and funding communities have rapidly initiated over 500 covid-19 related trials (https://clinicaltrials.gov/ct2/who_table). these clinical trials have been fasttracked by ethical committees worldwide and a range of therapeutic interventions registered on clinical trials.gov are taking forward phase 1, 2 and 3 trials of antiviral drug regimens, biologics, repurposed drugs in various combinations, herbal remedies, nutritional supplements, and cellular therapies. the results of ongoing clinical trials of new antiviral regimens, biologics and repurposed drugs (in various combinations) are eagerly awaited. we focus this editorial specifically on the background to, and the rationale for, the use and evaluation of mesenchymal stromal (stem) cells (mscs) in treatment trials of patients with severe covid-19 disease. this is an area which has been eclipsed by the current emphasis the huge number of trials evaluating new anti-viral drugs, repurposed drugs and combinations thereof. defining the underlying pathogenesis and pathology of covid-19 disease for developing appropriate therapeutic interventions may prevent end organ damage and long-term functional disability in those who survive severe disease. autopsy and minimally invasive biopsy studies indicate that covid-19 is a multi-system disease. the lungs in particular manifest significant pathological lesions, such as alveolar exudative inflammation and interstitial inflammation, alveolar epithelium proliferation and hyaline membrane formation (menter t et al, 2020; tian s et al, 2020) . significant proliferation of type ii alveolar epithelia and focal desquamation of alveolar and bronchial epithelia and hyaline membrane formation j o u r n a l p r e -p r o o f are seen (xu et al 2020) ; with predominantly macrophage and monocyte immune cell infiltration in alveoli with multinucleated giant cells; lymphocytes (mostly cd4-positive t cells), and some eosinophils and neutrophils. the blood vessels of alveolar septum were congested, edematous and widened, with modest infiltration of monocytes and lymphocytes. hyaline thrombi in microvessels and focal hemorrhage in lung tissue, organization of exudates, and pulmonary interstitial fibrosis have been observed. furthermore, degeneration and necrosis of parenchymal cells and formation of hyaline thrombus in small vessels were observed in other organs and tissues (menter t et al, 2020; tian s et al, 2020) . immunohistochemical staining showed alveolar epithelia and macrophages positive for sars-cov-2 antigen. evidence of sars-cov-2 antigens in other organs and tissues has been detected which suggests that host immune responses evoked by sars-cov-2 infection are involved in the pathogenesis of multi-organ injury (yao et al, 2020) . covid-19, like mers and sars, is a systemic illness with multi-organ involvement. sars-cov-2 enters the host cells via the cell surface angiotensin converting enzyme 2 (ace2) receptor on the target cell surface . ace2 as a cardio-regulator, so there are numerous cells with ace2 receptors in blood vessels, alveolar type ii cells (at2) in the lungs and several other organs, such as heart, kidneys. it appears that all three lethal zoonotic coronaviruses, mers-cov, sars-cov and sars-cv-2 seem to induce excessive and aberrant host immune responses which are associated with severe lung pathology leading to acute respiratory distress syndrome (ards) li g et al, 2020; li g et al, 2020) . characteristic findings on chest imaging in covid 19 include bilateral ground glass and consolidative changes ). an associated cytokine storm may play a role in pathogenesis. elevated proinflammatory cytokines and chemokines including tumour necrosis factor (tnf)α, interleukin 1β (il-1β), il-6, granulocyte-colony stimulating factor, interferon gamma-induced protein-10, monocyte chemoattractant protein-1, and macrophage inflammatory proteins 1-α were significantly elevated in covid-19 patients. (huang c et al, 2020; liu j et al, 2020) . patients with evidence of hyperinflammation have an increased risk of mortality (mehta et al, 2020; ruan et al, 2020) . in those who survive intensive care, the long-term consequences of these aberrant and excessive immune responses may lead to long term pulmonary damage and fibrosis, with functional disability and reduction of quality of life. it is important that therapeutic interventions which can dampen the excess j o u r n a l p r e -p r o o f inflammation, thus preventing end organ damage and long-term functional disability in those who survive severe disease. for the past decade the medical and pharma communities have focused on developing therapeutics targeting the pathogen rather than on the role of underlying host factors (zumla et al 2016a; 2016b) . human immune defenses are dependent on a complex array of mechanical, innate and acquired immune mechanisms and any disturbance of this internal lung milieu results in serious and fatal consequences. improved understanding of inflammatory and immune pathways governing protective or deleterious outcomes, provide novel opportunities to target specific pathways that mediate immune pathology (figure 1 ). (https://ipscell.com/rmat-list). in 2018 the first allogeneic msc product received marketing approval in the european union. since some commercial stem cell clinics are marketing dubious therapies for cardiovascular disease and cancer (sissung & figg 2020) there are fda and cdc cautions regarding their use (https://www.fda.gov/consumers/consumer-updates/fda-warns-about-stem-cell-therapies) (https://www.cdc.gov/hai/outbreaks/stem-cell-products.html). mesenchymal stromal cells interact with most of the cell types of the innate and acquired mscs also express atpases and possess ecto-nucleotidase activity through cd73 expression, through which they have the capacity to deplete atp.. the immunomodulatory effects of mscs may also be triggered further by the activation of tlr receptor in mscs, which is stimulated by pathogen-associated molecules such as lps importantly, mscs do not have an ace2 receptor, which makes them immune to sars-cov-2. whilst generally regarded as safe (editorial, 2019), mscs are not immunologically inert as previously thought (lohan o et al, 2017; ankrum ja et al, 2014) . a recent systematic review j o u r n a l p r e -p r o o f and meta-analysis of intravascular msc therapy reviewed 55 randomised controlled trials of msc therapy compared to controls (thompson m, et al, 2020) , mscs compared to controls were associated with an increased risk of fever but not non-fever acute infusional toxicity, infection, thrombotic/embolic events or malignancy. (1, 5 and 10 x 10 6 cells/kg) recruiting a total of 9 patients (3 patients per dose cohort). msc infusion was associated with mild adverse reactions in 3 patients however no serious treatment related adverse events were identified. mscs are now being used as a potential therapy for treating covid-19 patients in order to reduce mortality. although the use of mscs has been found to be safe when used for treatment of other diseases, it is important to evaluate whether they are safe to use the excessive host response seen in patients with covid-19 appears to have induced a paradigm shift in longstanding focus of drug treatment interventions targeting the pathogen (sars-cov-2 in this case) to targeting the host response. currently, clinicaltrials.gov and the world health organization international clinical trials registry platform (who ictrp) report a combined 28 trials exploring the potential of mscs and their products for treatment or prevention of covid-19. table 1 lists clinical trials of mscs or their products which have been registered on clinicaltrials.gov. not all of the registered trials will be pursued and in recent weeks, five trials registered on the chinese clinical trial register ("chictr") and one trial registered on clinicaltrials.gov have been marked as "cancelled by the investigator". xxxxx) is open to any interested parties to join us to help define optimal msc therapy regimens and change the course of covid-19 and sustain the growing portfolio of cellular therapies for a range of acute and chronic infectious diseases. viable mscs rescue injured cells by mitochondrial transfer and produce a broad array of immuno-modulatory cytokines. mscs may be taken up by phagocytic cells -that may prolong and augment their biological effect after intravenous delivery. risks include generally reduced immune -competence including anti-viral/bacterial/fungal activity, as well as potential pro-tumorigenic effects. beneficial reduction of pro-inflammatory cytokines, 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of the therapeutic era? concise review cell therapy in acute respiratory distress syndrome clinical features of patients infected with 2019 novel coronavirus in wuhan, china the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china severe acute respiratory syndrome: historical, epidemiologic, and clinical features human mesenchymal stem cells inhibit differentiation and function of monocyte-derived dendritic cells ct-04βsafety and efficacy of allogeneic umbilical cord-derived mesenchymal stem cells (mscs) in patients with systemic lupus erythematosus: results of an open-label phase i study multipotent mesenchymal stromal cells and the innate immune system microbes as master immunomodulators: immunopathology, cancer and personalized immunotherapies transplantation of ace2 -mesenchymal stem cells improves the outcome of patients with covid-19 pneumonia coronavirus infections and immune responses sars-cov-2 and viral sepsis: observations and hypotheses longitudinal characteristics of lymphocyte responses and cytokine profiles in the peripheral blood of sars-cov-2 infected patients anti-donor immune responses elicited by allogeneic mesenchymal stem cells and their extracellular vesicles: are we still learning? potential effects of coronaviruses on the cardiovascular system: a review treatment with allogeneic mesenchymal stromal cells for moderate to severe acute respiratory distress syndrome (start study): a randomised phase 2a safety trial covid -19: consider cytokine storm syndromes and immunosuppression middle east respiratory syndrome post-mortem examination of covid19 patients reveals diffuse alveolar damage with severe capillary congestion and variegated findings of lungs and other organs suggesting vascular dysfunction the long-term impact of severe acute respiratory syndrome on pulmonary function, exercise capacity and health status intravenous mesenchymal stem cells prevented rejection of allogeneic corneal transplants by aborting the early inflammatory response mesenchymal stem cell perspective: cell biology to clinical progress: npj regenerative medicine presenting characteristics, comorbidities, and outcomes among 5700 patients hospitalized with covid-19 in the new york city area clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan radiological findings from 81 patients with covid-19 pneumonia in wuhan, china: a descriptive study stem cell clinics: risk of proliferation the dying stem cell hypothesis: immune modulation as a novel mechanism for progenitor cell therapy in cardiac muscle pathological study of the 2019 novel coronavirus disease (covid-19) through postmortem core biopsies cell therapy with intravascular administration of mesenchymal stromal cells continues to appear safe: an updated systematic review and metaanalysis ex vivo expanded mesenchymal stromal cell minimal quality requirements for clinical application mesenchymal stem cells: mechanisms of potential therapeutic benefit in ards and sepsis immunomodulation by mesenchymal stem cells (mscs): mechanisms of action of living, apoptotic, and dead mscs mesenchymal stem (stromal) cells for treatment of ards: a phase 1 clinical trial pathological findings of covid-19 associated with acute respiratory distress syndrome the pathogenesis and treatment of the `cytokine storm' in covid-19 human umbilical cord-derived mesenchymal stem cells for acute respiratory distress syndrome angiotensin-converting enzyme 2 (ace2) as a sars-cov-2 receptor: molecular mechanisms and potential therapeutic target treatment of acute respiratory distress syndrome with allogeneic adiposederived mesenchymal stem cells: a randomized, placebo-controlled pilot study clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study coronaviruses -drug discovery and therapeutic options reducing mortality from 2019-ncov: hostdirected therapies should be an option host-directed therapies for infectious diseases: current status, recent progress, and future prospects need for a global consortium for conduct of multicenter clinicals trails of cellular therapies for defining priorities, common protocols, frequent scientific exchange, and long term collaborative efforts. an international consortium between clinical cancer and infectious disease research investigators (website: xxxxx) (this consortium network is open to any interested parties to join us to help define optimal msc therapy regimens and change the course of covid-19 and sustain the growing portfolio of cellular therapies for a range of acute and chronic infectious diseases) rnaseq data / proteomics shared or centrally conducted from mscs products to gauge for better definition of cellular products. differences in gene expression / proteomics in freshly prepared versus cryopreserved and subsequently thawed msc? definition of micrornas in mscs. investigator -initiated studies and commercial products-use different tissue origins and culture methods that may lead to different msc phenotypes and gene expression patterns. difference of 'edited', e.g. cytokine-edited mscs b. host responses: rnaseq expression pattern, immuno-phenotyping and functional t-cells assays gauging immuno-competence (e.g. anti-cmv responses) in longitudinally sampled blood prior and after msc infusion to gauge for systemic msc effects c. measuring cmv dna tagging or barcoding mscs. better understanding of msc-moa, e.g. phagocytosis of mscs by macrophages and systemic effects differences in dendritic cells and macrophage responses in vitro and ex vivo using viable msc or msc-derived products (e.g. exosomes, apoptotic bodies). gauging the most suitable and safest msc profile for covid-19 treatment smart clinical studies to address different modes of msc delivery, e.g. single or repeated doses, escalating dosing? improved clinical efficacy by repeated infusions? role of identical msc donor in repeated dosing? increased efficacy and safety if mscs are used from different donors in the case of repeated infusions ? conditioning' patients prior to mscs delivery. can msc-associated effects be improved by using repurposed drugs or biologicals that would augment the desired mscs effects, e.g. decreasing damaging inflammation which patients benefit most from msc treatment ? concise clinical documentation needed concerning patients with covid-19 that allows comparison of trials. differences associated with msc products (viable, msc -apoptotic bodies, exosomes), (covid-19), disease status or the patients phenotype (e.g. high il-6 or il-17 levels) ? role of lymphopenia in response to mscs ? smarter patient selection associated with pathophysiology may aid to offer improved treatment modalities attracting pharma and funder attention: convincing donors that cellular therapies are viable options for the adjunct treatment of patients with covid-19 and other lethal infectious diseases 6. gathering trials evidence base on msc therapy for covid-19 (the acronym 'doses': d = donor, o=origin, s=separation method, e= exhibited characteristics, s= site of delivery has been proposed to define optimal mscs therapy adverse events monitoring and analysis: short term and long-term folllowup of patients, e.g. short term analysis of general immuno-competence (e.g. anti-cmv and anti-sars-cov-2 humoral and cellular responses, long term observation concerning infectious complications creation of biobanks and access to biological material from patients with covid-19 infection: creating repository of samples obtained during msc trials eg blood samples (or bal) for unbiased gene expression analysis, proteomics and molecular analysis of t-cell responses, e.g defined by deep tcr sequencing to gauge for msc effects, different reactivity and biology of neutrophils, macrophages and dendritic cells from patients with covid-19 as compared to non-covid-19 patients? synoptic view with other, complementary assays gauging pulmonary recovery advancing the global consortium activities to f application of mscs for other infectious diseases key: cord-268883-nf4fm7r7 authors: corchuelo, jairo; ulloa, francisco chavier title: oral manifestations in a patient with a history of asymptomatic covid-19. case report date: 2020-09-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.071 sha: doc_id: 268883 cord_uid: nf4fm7r7 the pandemic situation has led to public health measures that have forced patients with and without the sars-cov-2 virus to remain isolated and take steps to prevent the spread. many of these patients have been unable to attend the control of medical-dental services, which in many cases complicates their situation. this study reports on the oral manifestations of an asymptomatic covid-19 patient treated interdisciplinary by teleconsultation due to the sudden appearance of lesions in the oral mucosa. lesions are diagnosed, therapeutic measures are taken, and improvement is shown. this case shows that the problems that arise in the oral mucosa in patients with suspected or confirmed sars-cov-2 infection can be monitored through interdisciplinary teleconsultation during the pandemic with the support of information technology currently available worldwide. it also decreases the risk of transmission of sars-cov-2 between patients and health professionals. sars-cov-2 is a respiratory coronavirus, zoonotic disease having both bats and pangolins as the most probable origin and intermediate host (association 2020; chan et al. 2020) . is believed to be spread through close person-to-person contact (about 2 meters), a distance at which the respiratory droplets from an infected person either symptomatic or asymptomatic that coughs, sneezes, or speaks can spread to other people who do not have adequate barriers. another route of transmission occurs indirectly when saliva droplets fall on other surfaces, such as the ground and objects made of different materials, and people come into contact with them (kwok et al. 2015) . their mortality is independent of their immune status (mehta et al. 2020) ; the virus is resistant to standard defenses that do not appear to respond efficiently to inflammatory invasion and cytokine storm (guo et al. 2020 ). lymphocytopenia and t-cell over-activation with reduction of an effective humoral / cellular immune response have been reported in covid-19 patients(dziedzic and wojtyczka 2020; xu et al. 2020 ). dysfunctions such as anosmia and ageusia have been found as inflammation-induced symptoms of covid-19 (petrescu et al. 2020 ). due to the use of intensified therapeutic methods possibly aggravated by sars-cov-2, an increase in cases with oropharyngeal symptoms / conditions, dental-oral problems associated with soft tissues, saliva production (dry mouth) as side effects, could be predicted, even after recovering from covid-19. the candida albicans is a normal inhabitant in many mouths, diagnostic confirmation of infection is often based on a successful response (i.e., resolution of lesions) to antifungal medications. this form of diagnostic confirmation can be further enhanced by culturing the pathogen, preparing a fungal smear, or even an incisional biopsy (zegarelli 1993 ). immunoinflammatory processes have been associated with hyperpigmentation of melanin from the oral mucosa (chandran et al. 2016) . different factors produced during inflammation, such as prostaglandins, leukotrienes, cytokines, and inflammatory mediators, may play a role in this response and increased melanogenesis (taylor et al. 2009; lambert et al. 2019) . inflammation mediators, such as histamine and arachidonic acid metabolites, trigger melanogenesis (mackintosh 2001 ) and inflammatory cytokines such as tnf-α and il-1α induce j o u r n a l p r e -p r o o f the secretion of melanogenic agents (scf, hgf, bfgf, endothelin) by keratinocytes (feller et al. 2014 ). together, these agents explain the melanin pigmentation that is sometimes seen in association with inflammatory conditions of the skin or oral mucosa (satomura et al. 2007 ). physiological melanin pigmentation of the oral mucosa occurs most frequently in the gingiva and does not transgress the mucogingival junction (meleti et al. 2008) . pigmentation is more extensive in the anterior part of the mouth than in the posterior part and on the labial / labial surfaces (feller et al. 2014 ). the objective of this brief article was to report a relevant case of oral manifestations in an asymptomatic patient with covid-19. 40-year-old female patient who works as assistant manager in a bank in new york (usa) who attends the teleconsultation (cali-colombia) accompanied by her husband and manifests the presence of reddish plaques on the lower lip and the appearance of dark brown pigmentation in the gum of 8 days of evolution. in the teleconsultation, the patient presented a photo of the lower lip ( fig.1a) . she is asked for authorization to observe the injury through the mobile phone and the husband is asked to operate the camera and take photographs of different points of the mouth. during the anamnesis the patient indicates that she have been taking the following medications: ibuprofen which is taken occasionally for headache, vitamin d2 (1 pill every week), and j o u r n a l p r e -p r o o f azithromycin which she took in 2 instances for five days (3 weeks and 1 week prior to the dental teleconsultation) prescribed by his primary care doctor through telehealth, since he had lymphadenopathy at the neck level, in addition to having tested positive for the antibodies (sars cov 2 ab igg positive) three weeks before the dental teleconsultation and her husband was diagnosed with covid-19 six weeks before. the patient states that her husband, with whom she cohabits, is a health care worker that had acquired the infection in the hospital by working with patients with covid-19 at the height of the pandemic in the first half of 2020 in new york. he was tested multiple times presenting a positive rt-pcr tests (testing was performed using the cobas 8800 sars-cov-2 test.) and positive antibodies for covid-19 (testing was performed using the chemiluminescent immunoassay). the patient reports that her husband was symptomatic with a fever greater than 38°c and he was in disability for 52 days. minutes, then rinse with water and let the brush dry. the patient is contacted again by dental teleconsultation after 20 days, the oral cavity is verified by telephone and a recovery of the lesions of the lips is observed (fig. 1b) . she does not present aphthous ulcers and the whitish color of the tongue was significantly reduced (fig. 1f) . the recent photo, showing the melanin pigmentation in the attached gingiva of the anterior teeth, is compared with a photo taken 6 months before (figs.1 e, h) . this comparison shows that the patient did not have the pigmentations. it is explained to her that the pigmentation is related by her afro-descendant origin where this pigmentation is frequent and that the inflammatory process lived in response sars-cov-2 could cause the proliferation of melanocytes in that part of his body. it is left under observation for the next control. oral candida infection has been reported to almost always involve a locally or systemically compromised host (zegarelli 1993) . taking into account that candida albicans is part of the oral microbiome and that there were favorable events for its pathological development, such as the decrease in salivation manifested in the patient by the sensation of dry mouth, in addition to the frequent use of antibiotics and a mild predisposing factor such as the female sex (zegarelli 1993) and the successful response to nystatin treatment, we can clinically confirm candida infection the hyperpigmentation of the gums in the anterior teeth due to the aesthetic problem that it represents for the patient is the one that causes of most concern. the patient is fair-skinned and at the last follow-up appointment the patient stated: "i feel happy because the lesions on the lip and tongue disappeared with the treatment, and i will be reviewing the evolution of the gum pigmentation until the next control appointment." in conclusion, we can affirm that the problems that arise in the oral mucosa in patients with suspected or confirmed sars-cov-2 infection can be monitored through interdisciplinary teleconsultation during the pandemic with the support of information technologies available to many people worldwide, as demonstrated in this case with an asymptomatic patient with j o u r n a l p r e -p r o o f a familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster an update on the epidemiological characteristics of novel coronavirus pneumonia (covid-19) covid-19) -transmission face 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face medicine possible involvement of stem cell factor and endothelin-1 in the emergence of pigmented squamous cell carcinoma in oral mucosa pigmented lesions of the oral mucosa and perioral tissues: a flow-chart for the diagnosis and some recommendations for the management oral surgery, oral medicine, oral pathology, oral radiology, and endodontology oral erosions and petechiae during sars-cov-2 infection oral mucosal lesions in a covid-19 patient: new signs or secondary manifestations? oral vesiculobullous lesions associated with sars-cov-2 infection. oral diseases [internet treatment of severe physiologic gingival pigmentation with free gingival autograft. quintessence international black and brown: non-neoplastic pigmentation of the oral mucosa. head and neck pathology beneficial actions of melatonin in the management of viral infections: a new use for this "molecular handyman oral manifestations, counts of cd4+ t lymphocytes and viral load in brazilian and american hiv-infected children authors' contributions: corchuelo j: conceptualization, study design, clinical studies, literature key: cord-308080-1heu9vuv authors: simulundu, edgar; mupeta, francis; chanda-kapata, pascalina; saasa, ngonda; changula, katendi; muleya, walter; chitanga, simbarashe; mwanza, miniva; simusika, paul; chambaro, herman; mubemba, benjamin; kajihara, masahiro; chanda, duncan; mulenga, lloyd; fwoloshi, sombo; shibemba, aaron lunda; kapaya, fred; zulu, paul; musonda, kunda; monze, mwaka; sinyange, nyambe; liwewe, mazyanga m.; kapin’a, muzala; chipimo, peter j.; hamoonga, raymond; simwaba, davie; ngosa, william; morales, albertina n.; kayeyi, nkomba; tembo, john; bates, mathew; orba, yasuko; sawa, hirofumi; takada, ayato; nalubamba, king s.; malama, kennedy; mukonka, victor; zumla, alimuddin; kapata, nathan title: first covid-19 case in zambia – comparative phylogenomic analyses of sars-cov-2 detected in african countries date: 2020-10-06 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1480 sha: doc_id: 308080 cord_uid: 1heu9vuv since its first discovery in december 2019 in wuhan, china, covid-19, caused by the novel coronavirus sars-cov-2, has spread rapidly worldwide. whilst african countries were relatively spared initially, the initial low incidence of covid-19 cases was not sustained for long due to continuing travel links between china, europe and africa.. in preparation, zambia had applied a multisectoral national epidemic disease surveillance and response system resulting in the identification of the first case within 48 hours of the individual entering the country by air travel from a trip to france. contact tracing showed that sars-cov-2 infection was contained within the patient’s household, with no further spread to attending health care workers or community members. phylogenomic analysis of the patient’s sars-cov-2 strain showed it belonged to lineage b.1.1., sharing the last common ancestor with sars-cov-2 strains recovered from south africa. at the african continental level, our analysis showed that lineage b.1 and b.1.1 lineages appear to be predominant in africa. whole genome sequence analysis should be part of all surveillance and case detection activities in order to monitor the origin and evolution of sars-cov-2 lineages across africa. the who declared covid-19, caused by sars-cov-2 a public health emergency of international concern (pheic) on 30 th january 2020 and later a pandemic on 11 th march 2020. 1 as of 28 th september, 2020 there were 32.7 million covid-19 cases with 991,000 deaths worldwide reported to the who. 2 all african countries have been affected and have reported a total of 1,172,342 covid-19 cases including 25,481 deaths. 2 as the global covid-19 events unfolded, and africa's first covid-19 case was reported from egypt on 14 th february 2020, many african countries prepared for the arrival of covid-19. 3 zambia embarked on the intensification of the disease surveillance and emergency preparedness and response systems, including activating the public health emergency operations centre (pheoc). as part of preparedness activities, ports of entry were put on alert and thermal scanners were installed for screening incoming passengers at airports and ground crossing. key to the preparedness was ensuring that local and international networks were functional, including staff training and were crucial for early detection of imported cases given that zambia was at risk for importation of covid-19. 4 the university teaching hospital (uth) virology biosafety level-2 (bsl-2) laboratory, and the university of zambia school of veterinary medicine bsl-3 laboratory in lusaka, zambia were identified as national covid-19 diagnostic testing centers and for molecular analyses of sars-cov-2 lineages. we report the identification and clinical management of the first covid-19 case from zambia, and present the phylogenetic analyses of the patient's sars-cov-2 isolate, comparing it to other sars-cov-2 lineages reported from other african countries. ethical review and approval to publish: ethical approval for case study and phylogenomic sequencing, and publication of this case study was obtained from the university of zambia positive only in the case under study. further questioning indicated that the patient had a slightly dry and sore throat. on 18 th march, three days after returning to lusaka, our case developed a mild fever (38.0 o c) and was treated using paracetamol 1 gm three times a day orally for 5 days. similar to reports from europe and the usa 5-7 patient had anosmia and complained of a metallic taste in the mouth two days prior to complete loss of taste. our patient did not have any co-morbidities and was placed under quarantine for 21 days after testing positive to sars-cov-2. on day-5 (20 th march 2020), he developed a mild cough, persistent fever (>38 o c) , chest discomfort and clinical examination revealed bilateral chest crepitations. there were bilateral infiltrates on chest x-ray and full blood count showed mild lymphopenia (table 1, figure 1 ). he was thus classified as having 'moderate covid-19 pneumonia' and transferred for further clinical management at the national covid-19 specific hospital where he was isolated, and was given a course of azithromycin (and then switched to amoxycillin-clavunate acid) and supportive care. smell and taste abnormalities resolved within 5 days. the patient did not require intensive care and steadily improved with resolution of fever and resolution of infiltrates on repeat chest radiograph. he made a full recovery by day 21. repeated contact tracing within the household, showed his wife testing positive for sars-cov-2, but his children remained negative. there was no further spread to other family members or attending health care workers. nasopharyngeal and oropharyngeal swab specimens were collected on 16 th march 2020 in accordance with the cdc recommendations, 8 and samples were processed using standard rt-pcr methodology for sars-cov-2 detection. for whole genome sequencing, the sanger method was employed using several overlapping primers designed using geneious software version 10.0.9. the list of primers and their combinations for rt-pcr assays and sequencing are listed in table s1 . the complete genome of sars-cov-2 investigated in this study was deposited in genbank (accession no. mt790522). the whole sars-cov-2 genome generated in this study, together with other selected sars-cov-2 sequences accessed from gisaid data base were aligned using the fft-ns-2 algorithm available in the multiple sequence alignment program (mafft) using default settings. 9 the selection included mostly representation from all african countries that had deposited whole genomes in the gisaid database as of 30 th august, 2020. the resulting final alignment was then uploaded to the iq-tree webserver 10 for construction of a maximum likelihood phylogeny using the general time reversible nucleotide substitution model and rate of heterogeneity set to gamma (gtr+g), otherwise default settings. branch robustness was estimated using ultrafast bootstrapping tool available in iq-tree with 1000 replicates. 11 the ml tree was then rooted using tempest (version 1.5.1), 12 which estimated the best-fitting root of this phylogeny using the heuristic residual mean squared function, aimed at minimizing the variance of root-to-tip distances. the resultant ml tree file was edited using itol. 13 viral lineages were identified in the phylogeny according to the recently described nomenclature 14 as well as demonstrated recently in uganda. 15 phylogenomic analysis showed that the detected sars-cov-2 belonged to lineage b.1.1, sharing the most common recent ancestor with viruses detected in south africa (figure 2) wuhan-hu-1, which included the d614g mutation which has been observed to correlate with increased case fatality rates. 16 the sars-cov-2 reported in this study also had the p4715l mutation which has been observed to occur in almost all strains with d614g mutation, which might affect the speed of virus replication. 17 sars-cov-2 variants with p4715l predominate in europe and the usa. 17 whilst most (if not all) complete genomes of sars-cov-2 deposited in public databases were sequenced using next generation sequencing (ngs) platforms, we utilized the sanger method, which is more widely available in africa when compared to ngs. as laboratory capacities for ngs are yet to be developed in many african countries, the sanger method could still be used to sequence a number of complete genomes enough to provide a better understanding of the molecular epidemiology of sars-cov-2 in zambia. the epidemic preparedness and response in zambia remains on high alert for the covid-19 pandemic and capacity for contact tracing in the community has been built steadily over time due who 2020. report of the who-china joint mission on coronavirus disease is africa prepared for tackling the covid-19 (sars-cov-2) lessons from past outbreaks, ongoing pan-african public health efforts, and implications for the future preparedness and vulnerability of african countries against importations of covid-19: a modelling study alterations in smell or taste in mildly symptomatic outpatients with sars-cov-2 infection association of chemosensory dysfunction and covid-19 in patients presenting with influenza-like symptoms self-reported olfactory loss associates with outpatient clinical course in covid-19 interim guidelines for collecting, handling, and testing clinical specimens from persons under investigation (puis) for mafft online service: multiple sequence alignment, interactive sequence choice and visualization w-iq-tree: a fast online phylogenetic tool for maximum likelihood analysis ultrafast approximation for phylogenetic bootstrap exploring the temporal structure of heterochronous sequences using tempest (formerly path-o-gen) interactive tree of life (itol) v4: recent updates and new developments a dynamic nomenclature proposal for sars-cov-2 lineages to assist genomic epidemiology main routes of entry and genomic diversity of sars-cov-2 sars-cov-2 viral spike g614 mutation exhibits higher case fatality rate variant analysis of covid-19 genomes nosocomial outbreak of novel arenavirus infection a multisectoral emergency response approach to a cholera outbreak in zambia characterization of influenza a viruses isolated from wild waterfowl in zambia seroepidemiological prevalence of multiple species of filoviruses in fruit bats (eidolon helvum) migrating in africa influenza surveillance in zambia seroprevalence of filovirus infection of rousettus aegyptiacus bats in zambia marburgvirus in egyptian fruit bats an evaluation of the zambia influenza sentinel surveillance system emergence of genomic diversity and recurrent mutations in sars es, nk, az, jt, mb and az are members of the pan-africa-europe network for emerging and re-emerging infections (pandora-id-net) -website: https://www.pandora-id.net/partners).az is in receipt of a uk nihr senior investigator award, and 2020 mahathir science award.we would like to thank all laboratory staff from the national influenza center, virology laboratory, university teaching hospitals for technical assistance. port health staff and health care workers involved in identification and managing our case, respectively, are duly acknowledged.j o u r n a l p r e -p r o o f key: cord-280060-gzby85u9 authors: rello, jordi; manuel, oriol; eggimann, philippe; richards, guy; wejse, christian; petersen, jorgen eskild; zacharowski, kai; leblebicioglu, hakan title: management of infections in critically ill returning travellers in the intensive care unit—ii: clinical syndromes and special considerations in immunocompromised patients() date: 2016-04-28 journal: int j infect dis doi: 10.1016/j.ijid.2016.04.020 sha: doc_id: 280060 cord_uid: gzby85u9 this position paper is the second escmid consensus document on this subject and aims to provide intensivists, infectious disease specialists, and emergency physicians with a standardized approach to the management of serious travel-related infections in the intensive care unit (icu) or the emergency department. this document is a cooperative effort between members of two european society of clinical microbiology and infectious diseases (escmid) study groups and was coordinated by hakan leblebicioglu and jordi rello for esgitm (escmid study group for infections in travellers and migrants) and esgcip (escmid study group for infections in critically ill patients), respectively. a relevant expert on the subject of each section prepared the first draft which was then edited and approved by additional members from both escmid study groups. this article summarizes considerations regarding clinical syndromes requiring icu admission in travellers, covering immunocompromised patients. over the last 20 years, the increase in international travel, which has been intensified by the availability of low-cost flights, has facilitated the movement of an increased number of patients from areas with endemic diseases to distant regions. as a consequence, cities around flight hubs have been and are exposed to the rapid dissemination of imported infections, as was reported in the initial dissemination of hiv infection in north america, and more recently in the 2009 influenza pandemic. similarly, outbreaks of cholera have been reported in travellers after long distance flights, and tourism has also been associated with the dissemination of infections such as measles, rubella, diphtheria, typhoid fever, and chicken pox, in addition to malaria and haemorrhagic fevers. poor health conditions and crowding are associated with tuberculosis (tb), diarrhoea, tetanus, and other infectious events, which may be imported by migrants from areas devastated by war. immunocompromised patients encompass a growing population with increased susceptibility to infectious complications. because they live longer and have a better quality of life than ever before, they may have more opportunity to travel and potentially encounter travel-associated infections. it has been estimated that up to one third of solid-organ transplant (sot) recipients may travel to resource-limited countries within the first year post-transplant. 1 in a survey in north american transplant centres, up to 44% of haematopoietic stem cell transplant (hsct) recipients reported travel outside the usa and canada after transplantation. 2 a international journal of infectious diseases 48 (2016) 104-112 significant number of immunocompromised patients may also be migrants who may return to their countries of origin to visit friends and relatives, and may acquire travel-associated infections. the increased use of monoclonal antibodies for therapy in immunological and oncological diseases has created another at-risk population, although the actual risk of travel-associated infection in these patients is not well established. 3 data on the real risk of infection in immunocompromised travellers relative to the general travel population are scarce, 4 and particularly the risk of developing an illness severe enough to warrant admission to an intensive care unit (icu). the repatriation of immunocompromised patients from hospitals in destination countries also carries the risk of contamination of the receiving hospital with multidrug-resistant (mdr) microorganisms, which requires specific infection control measures. 5 this article also addresses certain specific syndromes, such as pneumonia and acute respiratory distress syndrome (ards) occurring after travel. this position paper is the second escmid consensus document on this subject and aims to provide intensivists, infectious disease specialists, and emergency physicians with a standardized approach to the management of serious travel-related infections in the icu or emergency department. this document is a cooperative effort between members of two european society of clinical microbiology and infectious diseases (escmid) study groups and was coordinated by hakan leblebicioglu and jordi rello for esgitm (escmid study group for infections in travellers and migrants) and esgcip (escmid study group for infections in critically ill patients), respectively. a relevant expert on the subject of each section prepared the first draft, which was then edited and approved by additional members from both escmid study groups. this article summarizes considerations regarding clinical syndromes requiring icu admission in travellers, covering immunocompromised patients. (table 1) the risk of infection in sot recipients varies according to multiple factors, namely the type of organ transplanted, the time from transplantation, and the type and dose of immunosuppressive drugs received. 6 during the first month post-transplant, infectious complications are mainly healthcare-associated. the most profound immunosuppression occurs between months 2 to 6; historically, this is the period in which most opportunistic infections were diagnosed, including herpesvirus infections (cytomegalovirus), pneumocystis jirovecii pneumonia, and invasive fungal infections. 7 however, with the use of universal antiviral preventive strategies and long-term co-trimoxazole prophylaxis, opportunistic infections are currently rarely seen. after 6-12 months, the risk of infection decreases significantly and infections over this period are usually community-acquired, except in the case of increased immunosuppression (due to allograft rejection or dysfunction) or in the case of chronic surgical complications. because the incidence of infection is higher early after transplantation, it is recommended to avoid travel during the first year. 8 hsct recipients are at increased risk for bacterial and fungal infections during the engraftment period in the first month posttransplant. in the case of graft-versus-host disease, cellular immunosuppression is the mechanism responsible for the development of viral infections (particularly cytomegalovirus, adenovirus, and bk virus) and invasive fungal infections. 9 after the second year post-transplant it is considered that the degree of immunosuppression is non-significant if the patient has not developed chronic complications. while the use of biological agents for the therapy of rheumatological and autoimmune diseases has increased considerably over recent years, data on the risk of infection are mainly limited to the use of anti-tumour necrosis factor (tnf) agents. several large cohort studies found patients receiving anti-tnf therapy to be at greatest risk of developing skin infections, although the overall risk of severe infections was similar to that of patients receiving other non-biological therapies. 10 a study from the netherlands assessed the risk of infection in 75 travellers receiving biological agents relative to their travelling companions. 4 immunocompromised patients were at significantly higher risk of developing skin infections, fatigue, and abdominal pain, but not fever, diarrhoea, or respiratory infections. of note, no serious infection developed during or after the trip in these patients. patients on anti-tnf therapy have an increased risk of developing mycobacterial infections, with several cases of disseminated tb with a fatal outcome reported in the literature. 11 cutaneous leishmaniasis has also been reported in patients on anti-tnf treatment. 12 the risk of bacterial and fungal infections in patients with an oncological condition is increased during the administration of chemotherapy and/or radiotherapy and/or immunotherapy, particularly during the period of neutropenia. 13 in contrast, the risk of infection is generally considered not to be increased some months after the conclusion of chemotherapy and in patients receiving hormone therapy. patients with haematological conditions, such as lymphoma or hodgkin disease, may, however, have some degree of cellular immunosuppression even months after the remission of the disease. asplenic patients are at significantly higher risk of infection with encapsulated bacteria, namely streptococcus pneumoniae, neisseria meningitidis, haemophilus influenzae, and capnocytophaga canimorsus. 14 thus, appropriate vaccination with conjugated vaccines is an essential preventive strategy in these patients. other potentially life-threatening infections that are more common in asplenic patients include salmonellosis, babesiosis, and malaria. while the risk of infection is higher during the first month following splenectomy, the increased risk persists for years. the risk of infection in asplenic patients depends on the underlying condition, being higher in patients with haematological diseases and in those in whom immunization may not be fully successful or is associated with suboptimal protection over long periods of time. such patients may be instructed to start empirical antibiotics targeted at encapsulated bacteria immediately if any clinical signs or symptoms of infection ensue. 15 there are few studies that have addressed the epidemiology and clinical manifestations of malaria in immunocompromised patients. the incidence of malaria was reported to be less than 1% in hsct recipients in an endemic country (pakistan); however, data on other immunosuppressive conditions and in travellers are missing. 15 despite the lack of prospective studies, it appears that malaria is associated with more severe outcomes in immunocompromised patients than in the general population. a recent systematic review found that up to 45% of published cases of malaria in sot recipients had at least one criterion for severe malaria (o. manuel, personal communication). importantly, malaria may develop through transmission from the organ donor, and as such there may not be a travel history. 16 a case of cerebral malaria with >50% parasitemia has been reported in a patient receiving infliximab; 17 however such severe disease can occur in patients not on biologicals as well. malaria can also be more severe in splenectomized patients due to the lack of clearance of intraerythrocytic parasites. the successful treatment of severe malaria in immunocompromised patients has been reported with the use of erythropheresis and artesunate. 18 the choice of the preventive strategy for malaria in immunocompromised travellers should be individualized, favouring antimalarial prophylaxis in patients travelling to intermediate-risk and high-risk regions. several cases of severe dengue in immunocompromised patients have been reported, mostly in patients in endemic countries. in a series of kidney transplant recipients in india, up to 37% of patients diagnosed with dengue had a severe course and died. 19 all presented with fever, thrombocytopenia, myalgia, and retro-ocular pain. in contrast, in a series of eight patients receiving biologicals who were diagnosed with dengue, none developed severe infection. 20 dengue fever was reported to be a frequent cause of febrile neutropenia in haematological patients in india, but this was not associated with worse outcomes. 21 early diagnosis is essential in immunocompromised travellers with clinical manifestations suggestive of dengue in order to initiate early appropriate supportive therapy. aggressive volume replacement within the first 24 h of icu admission is important to limit the development of multiple organ dysfunction syndrome and increase the probability of survival. travel-related fungal infections in immunocompromised patients are uncommon, but potentially associated with a severe course and increased mortality. 22 invasive travel-related fungal infections that have manifested with a severe course in sot recipients and hiv-infected individuals include disseminated penicillium marneffei infection, aspergillosis, histoplasmosis, and coccidioidomycosis. 23 in patients receiving monoclonal antibodies, severe travel-associated histoplasmosis has been associated with a 50% mortality rate, and in another report, malignancy was a risk factor for acquiring a cryptococcus gattii infection. 24 importantly some of these infections may have a long incubation period so the travel history may be underreported. as such, a detailed travel history should be sought in immunocompromised travellers who develop fever associated with pulmonary lesions and/or localized cutaneous or subcutaneous disease, and these patients should be investigated promptly and aggressively for the diagnosis of invasive fungal infections. 22 the risk of tb is increased in transplant patients, hiv-infected individuals, and in patients receiving biologicals, but the risk of travel-acquired tb in immunocompromised patients is not well established. screening for latent tb infection after travel to endemic regions in these patients might, however, identify patients at risk of developing active tb. leptospirosis is a common cause of fever in returning travellers, and can be associated with severe complications. in a series of nine hiv-infected patients with leptospirosis, 67% presented with severe sepsis and the mortality was 22%. 25 data on the severity of leptospirosis in other immunocompromised populations are lacking. nocardiosis in sot recipients is associated with a high incidence of disseminated disease, particularly with central nervous system involvement. strongyloidiasis in immunocompromised patients is a rare but potentially life-threatening condition. donor-derived or travelacquired infestation with strongyloides stercoralis is associated with a high mortality. 26 cases of chagas disease (trypanosoma cruzi) either as a consequence of reactivation of a latent infection not identified at the time of transplant (because an unrecorded travel history or stay in an endemic area) or by transmission through the organ donor, can also be associated with a high mortality. 27 furthermore, immunocompromised patients may be particularly susceptible to severe forms of west nile virus infection and tick-borne encephalitis, all of which should be actively sought in the workup of patients with central nervous system symptoms after returning from endemic areas. there have also been case reports of severe disease from other travel-associated infections, such as salmonellosis, vibrio parahaemolyticus, and visceral leishmaniasis in immunocompromised patients. there are many causes of respiratory failure and of ards. those that are specific to certain geographic regions and that may appear unexpectedly in travellers are less common, but are nevertheless extremely important because appropriate therapy requires a correct diagnosis, and some infections may have epidemic potential. the infectious causes in particular may not be recognized immediately because they may be out of their usual geographical context. those that can cause ards will be discussed briefly below. table 2 summarizes the main recommended antimicrobial regimens for specific organisms involved in ards in returning travellers. cap is the most likely cause of acute respiratory failure in returning travellers. the usual pathogens, such as s. pneumoniae, h. influenzae, mycoplasma pneumoniae, chlamydophila pneumoniae, legionella pneumophila, and viruses such as influenza and respiratory syncytial virus, are the most common culprits. however aspiration must be considered in the elderly and in those who have become inebriated whilst on holiday. less common pathogens such as staphylococcus aureus, avian influenza viruses such as h7n9 and h5n1, the middle east respiratory syndrome coronavirus (mers-cov), and gram-negative rods such as burkholderia pseudomallei must also be considered, as well as a few other pathogens that do not usually cause pneumonia, such as malaria. influenza viruses such as h1n1 and h3n2, which are currently circulating, are perhaps the most common travel-related infections, particularly in the unvaccinated, those travelling across hemispheres, and where the available vaccine does not cover a particular strain effectively. influenza is an acute illness manifested by pyrexia, cough, chills, myalgia, and fatigue. there can, however, be more severe complications, specifically pneumonia, especially in pandemic years. in the 2009 influenza a(h1n1)pdm09 pandemic, more than 18 500 deaths were reported, with global estimates 15 times higher. the primary risk factors were age (young to middle age; >60% were aged <65 years), morbid obesity, pregnancy, and an immunocompromised status. influenza also increases the risk of bacterial pneumonia, particularly that caused by s. pneumoniae and s. aureus. those with severe disease deteriorate acutely after 4-5 days, with profound hypoxemia, shock, and often multiple organ dysfunction syndrome. the pathological findings are of an intense inflammatory/ haemorrhagic pneumonia, the severity of which seems to be influenced by the presence or absence of associated bacterial cap. 28 any patient with the above features, particularly if unvaccinated or having travelled to another hemisphere during the winter season, should be investigated for influenza, with diagnosis based on throat swab or nasal wash and a commercial kit based on antigen or rt-pcr. 29 unfortunately there is very low uptake of influenza vaccine even amongst healthcare workers, and as such there remains a large pool of susceptible individuals. although not yet reported to have been transmitted from humans, avian influenza h5n1 and h7n9 remain a potential threat, particularly in southeast asia. travellers who have had contact with birds in the affected areas and who present with otherwise unexplained ards should be screened. h5n1 has been reported from 17 countries and is currently most prevalent in egypt. 30 staphylococcus aureus pneumonia is usually a fulminant disease associated with rapid onset respiratory failure, frequently progressing to multiple organ dysfunction, shock, and death. complications are frequent and include pulmonary necrosis and abscess and empyema formation, particularly if the strain is a producer of panton-valentine leukocidin (pvl) toxin, a cytotoxin responsible for leukocyte destruction and tissue necrosis. risk factors are colonization or infection with s. aureus and a preceding influenza-like illness (ili). leucopenia (2.5 â 10 9 /l) is characteristic and may be an inverse biomarker of pvl burden. 31 both methicillin-sensitive s. aureus (mssa) and methicillinresistant s. aureus (mrsa) can cause cap. the latter is primarily a problem of recognition, as the organism is not prevalent in all countries and standard guideline-based therapies for pneumonia do not cover mrsa. the sensitivity profile of community-acquired mrsa differs from that of hospital-acquired mrsa in that it may be susceptible to macrolides, quinolones, clindamycin, and trimethoprim-sulfamethoxazole. therapy consists of appropriate antimicrobial therapy such as linezolid (possibly in preference to vancomycin, particularly if the strain is a pvl-producer), vancomycin, or ceftaroline. 32 pneumonia is the most common presentation of legionnaire's disease or legionellosis, and it may be severe, leading to multiorgan failure and death. characteristic clinical findings are relative bradycardia, hyponatremia, elevation in serum creatinine kinase, diarrhoea, confusion, and impaired liver and kidney function. 33 the recommended treatment regimen is macrolides or fluoroquinolones. 34 ten years after the severe acute respiratory syndrome (sars) epidemic that affected almost 8000 people and caused 775 deaths, mers-cov, a new coronavirus of the same family, appeared in saudi arabia and subsequently spread to nine countries in or near the arabian peninsula and 14 countries elsewhere. 35 on march 10, 2015, the world health organization global case count was 1060 laboratory-confirmed cases with 394 deaths (37%). all cases were resident in or had travelled to the middle east, most to saudi arabia, or had been in contact with travellers returning from these areas. mers-cov differs from sars-cov in that it binds to different receptors, and camels are thought to be the primary reservoir host, although the means of transmission from these animals is poorly understood. whereas transmission can occur between humans, the epidemic potential appears to be less. the disease is not always severe and symptoms range from an ili to severe pneumonia requiring mechanical ventilation. the most severely affected patients have mostly had comorbidities such as diabetes, renal failure, and chronic lung disease, or have been immunocompromised. 36 there is no specific antiviral treatment available for mers-cov infection. management is primarily supportive, directed towards the prevention of respiratory complications and infection control. corticosteroids are not currently recommended in this setting. it is still advised that those travelling to the middle east and who are at increased risk of severe disease should avoid contact with camels and their secretions, and avoid drinking raw camel milk (which will also prevent infection with brucella). all travellers should practice good hand and food hygiene, particularly where camels are present. a number of gram-negative pathogens may cause pneumonia and ards, in particular in relation to aspiration, or in association with ventilation where pathogens such as pseudomonas aeruginosa, acinetobacter baumannii, klebsiella pneumoniae, escherichia coli, and other enterobacteriaceae are of concern. 37 the latter include the extended-spectrum beta-lactamase (esbl)-and carbapenemaseproducers (such as those producing new delhi metallo-blactamase 1 (ndm-1)), which may be acquired during 'medical tourism'. 38 diagnosis requires a high index of suspicion and testing for the specific genes responsible for enzyme production. treatment remains a challenge due to deficiencies in the antibiotic pipeline. burkholderia pseudomallei is also a gram-negative bacillus endemic in southeast asia, northern australia, and possibly the indian subcontinent, southern china, hong kong, and taiwan. infection results from inoculation of contaminated soil and surface water through skin abrasions, with subsequent haematogenous spread. horizontal transmission also occurs, as well as transmission through the inhalation of polluted water. it is the most common cause of fatal community-acquired bacteraemia and pneumonia in certain areas of north-eastern thailand, as well as in darwin, australia. 39 travellers from endemic areas, especially in the wet season and particularly if there are comorbidities, are at risk. variable disease severity and the range of presentations (pneumonia, abscesses, osteomyelitis, and arthritis) make diagnosis a challenge. about 50% of patients present with pneumonia (which may appear as nodular infiltrates or air space consolidation), often with septic shock. the diagnosis is made when b. pseudomallei is cultured, but specific media are required. ceftazidime or meropenem with or without high-dose co-trimoxazole are the drugs of choice. although tb may occur in any patient, it seldom causes respiratory failure over a short period of time. yet, a recent prospective study from south africa reported that 1.5% of adults with active tb may require mechanical ventilation because of refractory hypoxemia, which in high tb prevalence countries translates into a significant burden of disease. 40 in this setting, 15% of tb suspects had confirmed tb, and it should be considered if the travel history involves relevant exposure. standard smear microscopy or culture are used for diagnosis, or rapid pcr if available (genexpert mtb/rif), which has been shown to have increased sensitivity and shorten the time to treatment. 41 where there is a high clinical suspicion of tb, empiric therapy should be initiated after adequate sampling has been obtained, particularly in the case of life-threatening or disseminated infection. initial therapy with four drugs (isoniazid, rifampicin, pyrazinamide, and ethambutol) is generally recommended where there is a low prevalence of resistance, and depending on the patient's origin and the results of the rapid detection of rpob gene mutations. patients with mdr-or xdr-tb need to be treated with second-line agents including aminoglycosides, quinolones, para-aminosalicylic acid, cycloserine, and clofazimine, and new drugs such as bedaquiline, linezolid, and delamanid. malaria, which is a frequent travel-related disease, may also lead to ards in severely affected patients. 41 increased alveolar capillary permeability may result in pulmonary oedema and respiratory failure either at presentation or after treatment. pregnant women are particularly at risk. slide microscopy and rapid antigen tests are the standard diagnostic tools, and the treatments of choice are the parenteral artemisinins, although resistance is emerging. non-infectious causes of bilateral pulmonary infiltrates with respiratory failure must be differentiated from infectious causes. these include cardiogenic pulmonary oedema, inflammatory pulmonary diseases such as cryptogenic organizing pneumonia (cop) and fibrosis, alveolar haemorrhage (including idiopathic granulomatous polyangiitis, lupus, and vasculitis), and ards from conditions such as eosinophilic pneumonia, pancreatitis, inhalational injury, and trauma. to identify these, clinical expertise is critical, along with the use of biomarkers (such a c-reactive protein, procalcitonin, and pro-b-type natriuretic peptide), serology to exclude autoimmune diseases, and imaging including echocardiography. if mechanical ventilation alone is inadequate, the use of neuromuscular blockade, recruitment techniques including prone ventilation, and veno-venous extracorporeal membrane oxygenation (ecmo) may improve oxygenation and the outcome. the berlin classification of ards severity is universally accepted and should be utilized to determine the site of therapy. 42 the acute physiology and chronic health evaluation (apache) score provides additional information regarding icu and hospital outcomes. 43 for pneumonia, the most frequently used scores are the pneumonia severity index (psi) and curb-65. to evaluate mortality risk in tb patients, the tbscore is useful and has been shown to predict the outcome. 44 haemorrhagic symptoms and fever can be caused by many infections due to bacteria, viruses, and parasites. disseminated intravascular coagulation (dic) may be a manifestation of severe septicaemia and can be caused by almost all gram-positive and gram-negative bacteria. dic is particularly present in septicaemia with n. meningitidis (figure 1 ), but is also seen in patients with s. aureus and s. pneumoniae bloodstream infections (figures 2 and 3 ). numerous viruses may also cause haemorrhagic symptoms, and these include dengue virus, crimean-congo haemorrhagic fever virus, ebola virus, yellow fever virus, hanta virus, and others (table 3) . it is most important to establish whether the patient has a history of travel within the past 4 weeks to areas where viral haemorrhagic fevers are endemic immediately at admission (table 3 ). if the history and the clinical features are suggestive, further details should be obtained, as shown in table 4 , and the patient should be evaluated as to whether isolation is necessary. in most countries where haemorrhagic fever viruses occur, malaria is also endemic, and a malaria test (rapid diagnostic test or microscopy) should be performed immediately and at the same time as blood cultures for bacterial infections are obtained. once malaria has been excluded, treatment should be started to cover a broad range of bacterial infections until such time as the diagnosis is confirmed. an example of gangrene related to severe staphylococcal septicaemia is shown in figure 2 . rapid assessment of the patient and isolation are key to limiting healthcare-associated transmission. the mers-cov outbreak in south korea illustrates how rapidly infections can spread in overcrowded hospitals. 45 most mers-cov cases in saudi arabia have also been linked to transmission in hospitals, 46 as was the case with sars-cov 47 and with crimean-congo haemorrhagic fever. 48 training of paramedical staff, nurses, and physicians, as well as guidelines for the recognition and rapid assessment of febrile patients at the initial point of contact, are essential, as is an isolation area for febrile patients with a relevant travel history. dic is an acquired condition of the vascular system leading to an uncontrolled systemic activation of the coagulation pathway. the generation of thrombin and fibrin may cause thrombotic occlusions of blood vessels, and hence organ injury and failure. 49 this is accompanied by an inflammatory reaction, further augmenting the coagulation process. dic frequently accompanies systemic inflammatory response syndrome (sirs), severe sepsis, trauma, and other conditions as diverse as anaphylaxis and heat stroke. [49] [50] [51] [52] [53] [54] the systemic activation of the clotting system is associated with the consumption of both coagulation factors and platelets, and as such, various combinations of platelet count, prothrombin time, activated partial thromboplastin time (aptt), a decrease in anti-thrombin (at) and protein c, as well plasma levels of fibrin and d-dimers have been used for the diagnosis. 55 a more standardized approach can be achieved by using the scoring system of the international society of thrombosis and haemostasis. 56 the successful therapy of dic is only possible when the underlying cause is identified and treated. the substitution of coagulation factors is currently unclear due to the lack of appropriate randomized placebo-controlled trials. the use of antifibrinolytics during dic should be avoided, as this drug class may lead to the deposition of fibrin in the vascular walls. 57 overall, the prevalence of dic during viral haemorrhagic fever is high and contributes to morbidity and mortality. early and effective treatment against the viral infection, if available, reduces the detrimental complications of dic. parameters for assessing dic and haemolysis are provided in table 5 . questions to be asked if the patient has travelled in an area where haemorrhagic fever occurs does the patient have a fever (>38 8c) or history of fever in the previous 24 hours? and has the patient cared for/come into contact with body fluids of/handled clinical specimens (blood, urine, faeces, tissues, laboratory cultures) from a live or dead individual or animal known or strongly suspected to have vhf? has the patient received a tick bite and/or crushed a tick with their bare hands and/or travelled to a rural environment where contact with livestock or ticks is possible in a cchf endemic area? has the patient lived or worked in basic rural conditions where lassa, ebola, or marburg fever is endemic, i.e., west/central africa or south america? has the patient travelled to any local area where a vhf outbreak has occurred? cchf, crimean-congo haemorrhagic fever; vhf, viral haemorrhagic fever. patients with suspected severe sepsis should be managed according to standard guidelines. 58 these include broad-spectrum antibiotics, aggressive initial fluid replacement, blood pressure support if needed, the correction of acidosis, and oxygenation by intubation and mechanical ventilation as needed. echocardiography is essential to evaluate cardiac function and any vegetations on the cardiac valves. in the initial stages it is difficult to differentiate between a viral haemorrhagic fever, severe bacterial sepsis, and severe malaria. travel patterns and risk behavior in solid organ transplant recipients international travel patterns and travel risks for stem cell transplant recipients international travel in the immunocompromised patient: a cross-sectional survey of travel advice in 254 consecutive patients symptoms of infectious diseases in immunocompromised 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pneumonia middle east respiratory syndrome (mers) interhuman transmissibility of middle east respiratory syndrome coronavirus: estimation of pandemic risk aetiological agents of ventilator-associated pneumonia and its resistance pattern-a threat for treatment risk factors for infections with extended-spectrum beta-lactamase-producing escherichia coli and klebsiella pneumoniae at a tertiary care university hospital in switzerland melioidosis: a review a randomised controlled trial of the impact of xpert-mtb/rif on tracheal aspirates nested within a burden of disease study in south african intensive care units managing malaria in the intensive care unit acute respiratory distress syndrome: the berlin definition. ards definition task force severity scoring in the critically ill: part 1-interpretation and accuracy of outcome prediction scoring systems tbscoreii: refining and validating a simple clinical score for treatment-monitoring patients with pulmonary tuberculosis middle east respiratory syndromeadvancing the public health and research agenda on mers-lessons from the south korea outbreak mers-cov outbreak in jeddah-a link to health care facilities cluster of severe acute respiratory syndrome cases among protected health-care workers-toronto, canada probable crimean-congo hemorrhagic fever virus transmission occurred after aerosol-generating medical procedures in russia: nosocomial cluster disseminated intravascular coagulation prospective validation of the international society of thrombosis and haemostasis scoring system for disseminated intravascular coagulation disseminated intravascular coagulation in trauma patients disseminated intravascular coagulation (dic) in cancer the obstetric patient and disseminated intravascular coagulation disseminated intravascular coagulation guidelines for the diagnosis and management of disseminated intravascular coagulation. british committee for standards in haematology towards definition, clinical and laboratory criteria, and a scoring system for disseminated intravascular coagulation prevention and treatment of major blood loss surviving sepsis campaign: international guidelines for management of severe sepsis and septic shock: 2012 the authors declare no conflicts of interest. jr and hl designed the manuscript: om and pe wrote the immunocompromised host section, gr and cw wrote the ards section, and cw, ep and kz wrote the haemorrhagic fever section. om and jr assembled the final version. all authors read and approved the last version of the manuscript. key: cord-279976-juz9jnfk authors: xie, mingxuan; chen, qiong title: insight into 2019 novel coronavirus — an updated intrim review and lessons from sars-cov and mers-cov date: 2020-04-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.03.071 sha: doc_id: 279976 cord_uid: juz9jnfk background: the rapid spread of the coronavirus disease 2019 (covid-19), caused by a zoonotic beta-coronavirus entitled 2019 novel coronavirus (2019-ncov), has become a global threat. awareness of the biological features of 2019-ncov should be updated in time and needs to be comprehensively summarized to help optimize control measures and make therapeutic decisions. methods: based on recently published literatures, official documents and selected up-to-date preprint studies, we reviewed the virology and origin, epidemiology, clinical manifestations, pathology and treatment of 2019-ncov infection, in comparison with severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) infection. results: the genome of 2019-ncov partially resembled sars-cov and mers-cov, and indicating a bat origin. the covid-19 generally had a high reproductive number, a long incubation period, a short serial interval and a low case fatality rate (much higher in patients with comorbidities) than sars and mers. clinical presentation and pathology of covid-19 greatly resembled sars and mers, with less upper respiratory and gastrointestinal symptoms, and more exudative lesions in post-mortems. potential treatments included remdesivir, chloroquine, tocilizumab, convalescent plasma and vaccine immunization (when possible). conclusion: the initial experience from the current pandemic and lessons from the previous two pandemics can help improve future preparedness plans and combat disease progression. in late december 2019, a pneumonia outbreak of unknown etiology took place in wuhan, hubei province, china, and spread quickly nationwide. chinese center for disease control and prevention (ccdc) identified a novel beta-coronavirus called 2019-ncov, now officially known as severe acute respiratory syndrome coronavirus 2 (sars-cov-2) (gorbalenya et al., 2020) , that responsible for the pandemic. this was the third zoonotic coronavirus breakout in the first two decades of 21 st century that allowing human-to-human transmission and raising global health concerns. chinese government had taken immediate, transparent and extraordinary measures, and reached initial achievements to control the outbreak. as of 11 march 2020, the pandemic in pubmed, web of science, embase, cnki, wanfang, vip, preprint biorxiv and medrxiv databases from the earliest available date to 11 march, 2020. initial search terms were "2019-ncov" or "2019 novel coronavirus" or "sars-cov-2" or "covid-19" or "corona virus disease 2019" or "ncp" or "novel coronavirus pneumonia". further search words were above keywords, "sars" or "sars-cov" or "severe acute respiratory syndrome", "mers" or "mers-cov" or "middle east respiratory syndrome", in combinations of with "spike protein" or "genome" or "reproductive number" or "incubation period" or "serial interval" or "fatality rate" or "clinical characteristics" or "pathology" or "autopsy" or "treatment". j o u r n a l p r e -p r o o f moreover, official documents and news released by national health commission of p.r. china, ccdc, cdc(usa) and who were accessed for up-to-date information on covid-19. only the articles in english or chinese were considered. in this review, we highlight the pandemic potential and pathological indications of emerging coronavirus, comprehensively and systematically summarize the up-to-date knowledge of the biological characteristics of 2019-ncov, including virology and origin, epidemiology, clinical manifestations, pathology and treatment. because of its natural structures and biological features to bind receptors on host cells, the spike protein of 2019-ncov may played an essential role in disease spreading. we summarized all of the four available pathology studies of covid-19 biopsy and autopsy, and compared the results with previous two deadly coronavirus diseases. new therapeutic measures are emerging one after another. potential effective treatments were remdesivir, chloroquine, tocilizumab, convalescent plasma and vaccine immunization (when possible). evidence-based medicine should always be advocated to guide our clinical decision. coronavirus belongs to the subfamily orthocoronavirinae in the family of coronaviridae in the order nidovirales, which mainly caused infections in respiratory and gastrointestinal tract. the 2019-ncov is a novel enveloped beta-coronavirus which has a single stranded positive sense rna genome . concerning the origin of the virus, several phylogenetic analysis suggested the bat to be the most probable animal reservoir. based on genome sequencing, 2019-ncov is about 89% identical to bat sars-like-covzxc21, 82% identical to human sars-cov and about 50% to mers-cov (chan et al., 2020; lu et al., 2020) . as both sars-cov and mers-cov were transmitted from bats to palm civets or dromedary camels, and finally to humans, there should be another animal representing as an intermediate host between bat and human. pangolins were suggested as the possible intermediate hosts, because their genome had approximately 85.5%-92.4% similarity to 2019-ncov, representing two sub-lineages of 2019-ncov in the phylogenetic tree, one of which (gd/p1l and gdp2s) was extremely closely related to 2019-ncov (lam et al., 2020) . other research suggested 2019-ncov was the recombinant virus of bat coronavirus and j o u r n a l p r e -p r o o f snake coronavirus, by comparison in conjunction with relative synonymous codon usage bias among different animal species (ji et al., 2020) . the truth is yet to be discovered. the spike surface glycoprotein of coronavirus plays an essential role in binding to receptors on host cells and determines host tropism. spike protein(s-protein) of 2019-ncov is reported to bind with angiotensin-converting enzyme 2 (ace2), the same receptor of sars-cov to invade host cells; whereas mers-cov uses dipeptidyl peptidase 4 (dpp4) as the primary receptor . the amino acid sequence another research team also discovered an "rrar" furin recognition site by an insertion in the s1/s2 protease cleavage site in 2019-ncov, instead of a single arginine in sars-cov. after quantifying the kinetics mediating the interaction via surface plasmon resonance, ace2 is calculated to bind to 2019-ncov ectodomain with ~15 nm affinity, which is approximately 10-to 20-fold higher affinity than ace2 binding to sars-cov (wrapp et al., 2020) . in all, the binding affinity between 2019-ncov s-protein and ace2 is comparable or even stronger than sars-cov s-protein and ace2. this may explain the rapid development and strong ability of human-to-human transmission in covid-19. the pandemic escalated exponentially at the beginning of 2020, which might only be the tip of the iceberg due to delayed case reporting and deficiency in testing kits . the onset of first cluster cases were reported an exposure history to the j o u r n a l p r e -p r o o f huanan seafood(wild animal) wholesale market in wuhan. however, phyloepidemiologic analyses suggested that huanan market was not the origin of 2019-ncov. the virus was imported from elsewhere and boosted in the crowded market (yu et al., 2020) . the proportion of infected cases without an exposure history and in health care workers gradually increased. all of the evidence indicated the human-to-human transmission ability of 2019-ncov, which may already be spread silently between people in wuhan before the cluster of cases from huanan market was discovered in late december. person-to-person transmission may occur mainly through droplet or contact transmission. according to guan's latest pilot study, 2019-ncov was detected positive in the gastrointestinal tract specimens (stool and rectal swabs) as well as in saliva and urine, and even in esophageal erosion and bleeding site of severe peptic ulcer patients . four important epidemiological parameters of 2019-ncov were reviewed in comparison with those of sars-cov and mers-cov(shown in table 1 ). representing the average number of new infections generated by an infectious person in a totally naïve population. for r0˃1, the number of infected is likely to increase; for r0 ˂1, transmission is likely to decline and die out. the reproductive number updated along with the development of the outbreak and interventions. r0 was estimated to be around 3 for sars (bauch et al., 2005) and ˂1 for mers (bauch and oraby, 2013) . the preliminary r0 of 2019-ncov was reported as 2.24-3.58 . several research groups reported estimated r0 of the outbreak depending on distinct estimation methods and the validity of underlying assumptions. liu et al. (2020) reviewed all of the 12 references of an estimated r0 ranged from 1.4 to 6.49, with a mean of 3.28 and a median of 2.79. in clinical studies, a 425-case study by 22 january 2020, reported an r0 of approximately 2.2(95%ci, 1.4-3.9) , while another 4021-case study by 26 january 2020, estimated 3.77(95%ci, 3.51-4.05) . the discrepancy may be due to sample number and different stages of the pandemic. incubation period is defined as the interval from initial exposure to an infectious agent to onset of any symptoms or signs it causes. a long incubation period may lead to a high rate of asymptomatic and subclinical infection. the first prediction of mean incubation period was 5.2 days (95%ci, 4.1-7.0 days), with the 95th percentile of the distribution at 12.5 days, based on 2019-ncov exposure histories of the first 425 cases in wuhan . a 4021-case study reported 4.75 days (interquartile range: j o u r n a l p r e -p r o o f 3.0-7.2 days) . another 88-exported-case study calculated the mean incubation period to be 6.4 days (95%ci, 5.6-7.7 days), using known travel histories to and from wuhan and symptom onset dates (backer et al., 2020) . all these literatures lay the foundation to set 14 days as the medical observation period if any exposure occurred. a latest study collected 1099 cases from 552 hospitals in 31 provinces in china and declared a median incubation period of 3.0 days, ranging from 0 to surprisingly 24.0 days. an adjustments in screening and control policies may be needed. the 2019-ncov generally has a longer incubation time than sars-cov (4.0 days, 95% ci 3.6-4.4 days) (lessler et al., 2009 ) and mers-cov (range 4.5-5.2 days) (park et al., 2018) . serial interval is the interval from illness onset in a primary case to illness onset in the secondary case. the mean serial interval was estimated at 7.5 days(95% ci, 5.3-19days) using contact tracing data from early wuhan cases in 2019-ncov pandemic, which was shorter than the 8.4-day mean serial interval reported for sars (lipsitch et al., 2003) and 12.6-day for mers (cowling et al., 2015) . another estimation of the mean serial interval from 26 infector-infectee pairs was surprisingly 2.6 days, which was shorter than the median incubation period, suggesting a substantial proportion of secondary transmission before illness onset (nishiura et al., 2020) . the cfr in early studies of covid-19 involving relatively small samples of confirmed cases in wuhan, varied from 4.3% to 14.6% huang et al., 2020; , but that may not be able to reflect the truth. the cfr in wuhan was undoubtedly higher than cfr outside of wuhan. the reported cfr ranged 1.4%-3.06% in large nationwide case studies . prognosis factors such as male, elderly patients aged≥ 60 years, underlying disease, severe pneumonia at baseline and a delay from onset to diagnosis >5 days substantially elevated the cfrs . cfrs in patients with cardiovascular disease, diabetes, hypertension and respiratory disorders were as high as 10.5%, 7.3%, 6.0% and 6.3%, respectively. according to who announcement, sars accounted for 8096 cases and 774 death, with a cfr of 9.6% (who, 2004 clinical presentation of covid-19 greatly resembled viral pneumonia such as sars and mers. most cases are mild cases(81%), whose symptoms were usually self-limiting and recovery in two weeks (wu and mcgoogan, 2020) . severe patients progressed rapidly with acute respiratory distress syndrome (ards) and septic shock, eventually ended in multiple organ failure. general information of four inpatient case studies with relatively comprehensive data were summarized in supplementary table 1. the 2019-ncov was more likely to infect elderly men with comorbidities. males were more susceptible to 2019-ncov infection, same as sars-cov and mers-cov studies (badawi and ryoo, 2016) , due to x chromosome and sex hormones' role on innate and adaptive immunity (jaillon et al., 2019) . chronic underlying diseases (mainly hypertension, cardio-cerebrovascular diseases and diabetes) may increase the risk of 2019-ncov infection , which is similar to mers-cov infection (badawi and ryoo, 2016) . smoking may be a negative prognostic indicator for covid-19 guan et al., 2020) . clinical information of the above four selected inpatient case studies were summarized in supplementary table 2. onset of symptoms were usually mild and nonspecific, presenting by fever, dry cough and shortness of breath. very few covid-19 patients had prominent upper respiratory tract and gastrointestinal symptoms (eg, diarrhea) huang et al., 2020) , compared to 20-25% of patients with mers-cov or sars-cov infection developed diarrhea (assiri et al., 2013) . however, only 43.8% of covid-19 patients had an initial presentation of fever, and developed to 87.9% following hospitalization , compared to as high as 99% and 98% frequent in sars-cov and mers-cov infection (badawi and ryoo, 2016) . those patients without fever or even asymptomatic may be left un-quarantined as silent infection source, if the surveillance methods focused heavily j o u r n a l p r e -p r o o f on fever detection. moreover, the onset of symptoms may help physicians identifying patients with poor prognosis. patients admitted to the icu were more likely to report pharyngeal pain, dyspnea, dizziness, abdominal pain and anorexia . in terms of laboratory findings, a substantial decrease in the total number of lymphocytes could be used as an index in the diagnosis of 2019-ncov infection, indicating a consumption of immune cells and an impairment to cellular immune function . non-survivors developed more severe lymphopenia over time . initial proinflammatory plasma cytokine concentrations were higher in covid-19 patients than in healthy adults. icu patients had even higher plasma levels of il2, il7, il10, gscf, ip10, mcp1, mip1a, and tnfα compared to non-icu patients . there were numerous differences in laboratory findings between patients admitted to the icu and those not, including higher white blood cell and neutrophil counts, higher levels of d-dimer, creatine kinase, and creatine in icu patients . typical chest ct manifestation of covid-19 pneumonia were initially small subpleural ground glass opacities that grew larger with crazy-paving pattern and consolidation. after two weeks of growth, the lesions were gradually absorbed leaving extensive opacities and subpleural parenchymal bands in recovery patients. however, guan et al. ( 2020) demonstrated that patients with normal radiologic findings on initial presentation consisted of 23.9% and 5.2% of severe and non-severe cases respectively, which add the complexity to disease control. (nicholls et al., 2003) . thrombi were seen in all six autopsies of sars-cov infected patients, with even huge thrombus formation in part of pulmonary vessels. coagulation function disorders were reported in most of the severe covid-19 patients, by elevated levels of d-dimer and prolonged prothrombin time, some of whom ended in disseminated intravascular coagulation huang et al., 2020; . this may explain some sudden death of clinical recovery patients and serve as an indication for disease severity. in an autopsy study, the only one patient without usage of corticosteroids demonstrated increased cd3+ lymphocyte than five other specimen treated by corticosteroids (pei et al., 2005) . it suggested an inhibition of immune system similarities. the human monoclonal antibody could efficiently neutralize sars-cov and inhibit syncytia formation between s-protein and ace2 expressing cells (sui et al., 2004) . appropriate modification of the monoclonal antibody may be effective for treatment of covid-19. what's more, potential therapies targeting the renin-angiotensin system, to increase ace2 expression and inhibit ace may be there are no effective antiviral treatment for coronavirus infection, even the strong candidates as lopinavir/ritonavir and abidol exhibited no remarkable effect on clinical improvement, day 28 mortality or virus clearance (chen et al., 2020) . expectation and attention were shifted to "remdesivir" which may be the most potential wide-spectrum drug for antiviral treatment of 2019-ncov. remdesivir is an adenosine analogue, which incorporates into novel viral rna chains and results in pre-mature termination. it is currently under clinical development for the treatment of ebola virus infection (mulangu et al., 2019) . wang et al. (2020b) revealed that remdesivir were highly effective and safe in the control of 2019-ncov infection in vero e6 cells and huh-7 cells. a successful appliance of remdesivir on the first 2019-ncov infected case in the united states when the his clinical status was getting worsen, were recently released (holshue et al., 2020) . animal experiments also showed superiority of remdesivir over lopinavir/ritonavir combined with interferon-β, by reducing mers-cov titers of infected mice and improving the lung tissue damage (sheahan et al., 2020) . the effectiveness and safety of remdesivir can be expected by the clinical trial lead by dr bin cao. the 2019-ncov infection is associated with a cytokine storm triggered by over-activated immune system xu et al., 2020b) , similar to sars and mers. the aberrant and excessive immune responses lead to a long-term lung function and structure damage in patients survived from icu. ongoing trials of il-6 antagonist tocilizumab, which shown effective against cytokine release syndrome resulting from car-t cell infusion against b cell acute lymphoblastic leukemia, may be expanded to restore t cell counts and treat severe 2019-ncov infection (le et al., 2018) . the available observational studies and meta-analysis of corticosteroid treatment suggested impaired antibody response, increased mortality and secondary infection rates in influenza, increased viraemia and impaired virus clearance of sars-cov and mers-cov, and complications of corticosteroid therapy in survivors (zumla et al., 2020) . therefore, corticosteroid should not be recommended for treatment of 2019-ncov, or use on severe patient with special caution. a review (nichol et al., 2003) . in conclusion, it still remains a challenging task to fight the 2019-ncov of unknown origin and mysterious biological features, and to control an outbreak of covid-19 with such a high r0, a long incubation period and a short serial interval, by limited treatment and prevention measures. lessons learned from the mers and sars outbreaks can provide valuable insight into how to handle the current pandemic. the successful public health outbreak response tactics of chinese government, such as hand hygiene, wearing masks, isolation, quarantine, social distancing, and community containment, can be copied by other countries according to their national situation. as the pandemic is still ongoing and expanding, experiences and research literatures from china and other countries will increase. the 2019-ncov should be monitored of any possible gene variation of antigenic drift or antigenic conversion, to avoid another round of outbreak. another lessons from this pandemic will be awe for nature and love for life. funding source: this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. ethical approval: the ethical approval or individual consent was not applicable. all authors declare no conflict of interest. all authors 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expression profiling of ace2, the putative receptor of wuhan 2019-ncov a novel coronavirus from patients with pneumonia in china reducing mortality from 2019-ncov: host-directed therapies should be an option crrt(%) 7 9 1.5 0.8 key: cord-290206-fmy4zrim authors: lim, jue tao; dickens, borame l; cook, alex r; khoo, ai leng; dan, yock young; fisher, dale andrew; tambyah, paul anantharajah; chai, louis yi ann title: the costs of an expanded screening criteria for covid-19: a modelling study date: 2020-08-12 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.025 sha: doc_id: 290206 cord_uid: fmy4zrim objectives: nosocomial infection is an ongoing concern in the covid-19 outbreak. the effective screening of suspected cases in the healthcare setting is therefore necessary, enabling the early identification and prompt isolation of cases for epidemic containment. we aimed to assess the cost and health outcomes of an extended screening strategy, implemented in singapore on 07 february 2020, which maximizes case identification in the public healthcare system. methods: we explored the effects of the expanded screening criteria which allows clinicians to isolate and investigate patients presenting with undifferentiated fever or respiratory symptoms or chest x-ray abnormalities. we formulated a cost appraisal framework which evaluated the treatment costs averted from the prevention of secondary transmission in the hospital setting, as determined by a branching process infection model, and compared these to the costs of the additional testing required to meet the criteria. results: in the base case analysis, an [formula: see text] of 2.5 and incubation period of 4 days, an estimated 239 (95% ci: 201-287) cases could be averted over 150 days within the hospital setting through esc. a corresponding $2.36 (2 – 2.85) million usd costs could be averted with net cost savings of $124 000 (95% ci: -334 000–516 000). in the sensitivity analyses, when positive identification rates (pir) were above 7%, regardless of [formula: see text] and incubation period, all scenarios were cost-saving. conclusion: the expanded screening criteria can help to identify and promptly isolate positive covid cases in a cost-saving manner or within acceptable cost margins where the costs incurred from the testing of negative patients could be negated by the averted costs. outbreak control must be sustainable and effective; the proposed screening criteria should be considered to mitigate nosocomial transmission risk within healthcare facilities. since its emergence in wuhan, hubei province, china, the coronavirus disease 2019 has continued to spread with an escalating numbers of cases and countries affected. 1 to prevent ongoing transmission, effective screening of suspected cases is necessary which enables the early identification and prompt isolation of cases for epidemic containment. these screening measures for testing have been largely guided by the world health organization's (who) case definitions, 2 which serves as a valuable epidemiologic tool for public health officials to track the disease and is regularly updated with the changing epidemiology and demographics of the disease. this definition includes the presentation triad of fever, chest symptoms as well as a positive contact with an active infection or travel to an area with confirmed local transmission. covid-19 shares many clinical similarities to other respiratory and febrile illnesses, creating significant uncertainty at the point of testing as to whether cases should be treated as a potential positive infection. although symptom case reports have emerged over the ongoing outbreak, [3] [4] [5] the case definition is dynamic, being continually updated using clinician feedback through research or policymakers who collate and publish. both pathways however have an inevitable time delay in information dissemination. this affects clinicians and healthcare workers (hcws) at the front line who rely on the case definition to screen and triage patients, where this epidemiologic case definition lag can lead to problems of case misclassification. the screening process should therefore maximise sensitivity to minimise the number of missed cases and risk of nosocomial transmission, which occurred in singapore during another coronavirus outbreak of severe acute respiratory syndrome (sars) in 2003. 6 during this outbreak, frequent inadequately protected patient-to-hcw interactions among untested and unidentified cases 6, 7 led to 97 hcws becoming infected. 8 due to the presence of nosocomial transmission, clinicians at the national university hospital, singapore (nuhs) quickly responded with a revised testing protocol. they screened patients with a substantial expansion of the admission and isolation criteria to quickly identify and isolate infected individuals whose symptom profiles were too mild to be considered for testing 9, 10 or for patients who sought medical attention with atypical disease presentations, especially in the pediatric or geriatric population. 11 the implementation of this expanded screening criteria (esc) placed all patients with undifferentiated fever or respiratory symptoms or chest x-ray abnormalities in isolation until all symptoms and fever were resolved or an alternative diagnosis was proven, regardless of travel history or confirmed previous exposure. using esc, nuh clinicians were able to identify and isolate 13 patients who did not fit the who sars criteria but were eventually confirmed to have sars, who would have otherwise been potential spreaders (the number of positive and negative cases for sars are presented in supplementary table 1.) 12 clinicians responded to the covid-19 crisis similarly, implementing esc on 7 th february 2020, which was approximately three weeks after the first imported case. with widespread concerns raised regarding the low detection rate of infected travellers where most present j o u r n a l p r e -p r o o f mild symptoms (12.1% with no fever, 67.7% with cough) 13 and high asymptomatic rates 14 an estimated 1.8% ascertainment rate in wuhan. 15 a wider screening policy for covid-19 and future novel respiratory viruses requires assessment in terms of its efficacy and costs. the clinical management and costs of a large proportion of negative outcomes comes at the expense of resources which can be invested in other parts of the healthcare system. the efficacy of the esc in long term should thus be assessed in terms of its prevention of nosocomial transmission which may not only negate these costs but also save resources for the healthcare system. this paper therefore assesses the practicality of esc through a cost-effectiveness analysis by estimating the number of cases that can be averted through esc, and calculating the associated costs from the testing of negatives and cost savings from potentially averted cases. the first case definition used by the ministry of health, singapore for the testing of suspect covid-19 cases was based on who and other international bodies recommendations. 16 this centered on the presence of fever, respiratory illness or pneumonia, and recent travel to wuhan, china (namely, regions with reported infections) or close contact with a case of covid-19 patient 17 (table 1 ). recognizing the limitations of these case definitions and extending from our experience from sars, 7,12 we proposed an expanded screening criteria (esc) simplified for execution at the hospital triage, which was then implemented on 7 february 2020 with immediate effect. any patients with undifferentiated fever or respiratory symptoms or chest x-ray abnormalities are placed into isolation on admission with respiratory precautions, investigated until symptoms and fever resolve or an alternative diagnosis was determined (table 1 ) we used our institution in singapore, a 1,000-bed tertiary hospital, as a study example. 18 as of 8 february 2020 to 21 february 2020, 14 cases have been identified through esc which would have otherwise been missed. we determined the total number of infected cases that could occur from each non-identified admitted covid-19 cases in a hospital setting using a branching process infection model (figure 1 ), which estimates the number of new infections at each generation. each day, a set of imported cases is designed to be able to start multiple generations of transmission. the model characterizes this influx of cases into the hospital and subsequent infections that may occur. the baseline generation represents the first covid-19 positive case which is not deemed to be a suspected case under the non-esc criteria (who criteria until 31 january 2020 or ministry of health criteria until 25 january 2020) but would otherwise have been isolated under esc. under non-esc screening, the daily influx of symptomatic and positive cases is parameterised by a binomial distribution with a probability determined by the positive identification rate (pir), otherwise referred to as the proportion of confirmed symptomatic cases observed out of the total number of observed respiratory illness cases . all symptomatic and asymptomatic cases are assumed to be able to transmit the infection due to the closed environment within the hospital setting so are not distinguished. the number of importations in the hospital facility is therefore, the number of infections incurred from these daily incoming non-isolated cases is determined by a poisson distribution with a rate of infection λ, and the incubation period length which determines the infectiousness period . therefore the total number of infections at time , to time and incubation period , is defined as, where , denotes the size of the generation descending from ancestor , and determined by, after each newly infected person's incubation period, the individual is assumed to be in the process of being identified and have a decreasing rate of infectiousness of 10% until their end point at 20 days. after the period + 1, an individual's infectiousness is consequently greatly reduced, where a person is expected to have follow up with the development of new symptoms or unexpected ongoing symptoms from the new infection of covid-19 and is consequently isolated, or if asymptomatic, is discharged. therefore, is updated to, for the main analysis, we ran 50 simulations with a set of parameters taken from literature; a rate of infection ( ) of 2.5 and incubation period (ip) of 4 days, 19 and pir rate 8.0% which is based on the upper bound for case identification in the sars epidemic in 2003. [20] [21] [22] [23] [24] [25] the full analysis was run for different parameter distributions (table 2) . for each independent combination, 50 simulations were run where the incubation period was varied between 4 to 8 days, the rate of infection λ from 1.5-3.5 increments, and the rate of influx from 1.0% to 30.0% in 1.0% increments based on a range of positive identification rates (pirs) from literature on covid-19, cov-sars and cov-middle east respiratory syndrome. [20] [21] [22] [23] [24] [25] all simulations were run across 150 days (approximately 5 months) and performed in r version 3.6.3. after determining the number of new cases occurring within healthcare facilities, we assessed the healthcare system costs and outcomes of implementing the proposed esc and followed the consolidated health economic evaluation reporting standards (cheers). the cost framework examined the impact of the esc on hospitalization and testing costs while considering the transmission dynamics and importation rates of covid-19 cases in a hospital setting. a constant daily influx of 84 patients was assumed across 150 days based on 1182 general ward patients being admitted across 14 days (8 february 2020 to 21 february 2020, supplementary table 2 ). the total number of patients being admitted to the isolation wards for undifferentiated fever or respiratory infection or an abnormal chest x-ray according to the esc was taken to be 14.7% (174 isolated out of 1182 admitted patients, supplementary table 2) . a proportion of these, according to the pir, will be covid-19 positive. all costs presented are in us dollars with no discounting for the year 2020. the net cost of esc is calculated as the total hospitalization costs for the isolation of negative patients subtracted from the total hospitalization costs averted from the isolation of positive cases which would have otherwise been missed by a non esc criteria. for the former, the total hospitalisation cost for the isolation of negative cases was the total number of negative diagnoses at the cost of $1201 each, as all patients receive 2 coronavirus polymerase chain reaction (pcr) tests and a respiratory isolation room cost (supplementary table 3 ). this represents the costs to the healthcare system which should be minimised as they require no further isolation measures. for the latter, the total costs averted from the isolation of positive cases under the esc was determined by the branching process model with an associated testing and treatment cost each. these covid-19 positive patients inherit the same initial costs as negative patients at the testing phase and have subsequent treatment costs depending on whether they require intensive care unit (icu) stay with a probability of 26.6% based on patient outcome profiles from literature. 4 table 4 ). patients who required icu received an additional cost for 7 days of intensive care management, followed by the standard respiratory isolation procedures for a non-icu patient at a total of $12 658 (supplementary table 5 ). the sponsor of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. the corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication. at an of 2.5 and incubation period (ip) of 4 days, approximate to estimates by wu and colleagues 29 for wuhan, an estimated 240 (95% ci: 200-290) cases would be prevented over 150 days through esc by isolating patients presenting fever or respiratory symptoms such as cough with their travel and exposure profile not considered (table 2) . with an observation of 84 patients being admitted per day into hospital and a corresponding total of 12 600 across the 150-day period (supplementary table 2 ), 1900 patients would be expected to enter respiratory isolation of which 200 (95% ci: 170-230) to 300 (95% ci: 250-370) would be covid-19 positive, depending on the ( table 2) . a total cost between $2.0 million (95% ci: 1.7-2.3 million) to $3.0 million (95% ci: 2.5-3.7 million) could be potentially averted from the isolation of these patients. a corresponding cost saving at an of 2.5 or greater can be achieved with $120 000 (95% ci: -330 000-520 000) to $740 000 (95% ci: 120 000 -1 400 000) saved. of note, if the proportion of positive cases is taken to be 8.0%, which represents the upper bound of sars patient identification during the testing period for the 2003 epidemic, 20-25 the total cost of testing for negative patients is $1.9 million at this pir. figure 3a) . a higher causes esc to yield larger cost savings with this difference in cost savings being more pronounced at higher pir values. at a pir of 1.0%, having an of 1.5 versus 3.5 increases the cost savings by $153 000 with 14 more infections averted ( figure 3b ) but at a pir of 30.0%, this difference widens to $5.0 million ( figure 3a ) with 440 more infections averted ( figure 3b ). however, provided that the pir is above 8.0%, regardless of , cost savings can be achieved through esc implementation. notably, less than a 3.0% difference was recorded in net cost savings across the of 1−3.5 at a pir of 1.0%, with the largest change being a -$49 000 decrease in net cost savings at the of 3.5. across all and pir values, changing the ip from 4 to 8 days decreased the net cost savings of esc by an average of -$52 000. j o u r n a l p r e -p r o o f discussion among the lessons learnt during the sars epidemic of 2003-2004 was the importance of adapting official case definitions to provide effective triage and screening, 7 especially as the definitions are expected to rapidly evolve for a new disease. for the current covid-19 outbreak, all early diagnosed patients had travelled from china but by the 4 th feb 2020, suspected local transmission was evident therefore negating the usefulness of this travel history 30 . furthermore, as symptom profiles were identified as being very heterogeneous with the two dominant symptoms fever and cough at 88.7% and 67.8% prevalence among 1099 patients in mainland china, 5 the expanded screening criteria (esc) was designed to capture all of these patients to reduce the risk of nosocomial transmission. as of 7 february 2020, esc was implemented as an emergency response to operate alongside intense contract tracing. 31 the results demonstrate that provided the positive identification rate (pir) is sufficiently high at 7% or greater, costs-savings can be created across the values 1.0−3.5, making the screening strategy sustainable for the healthcare system in the long term. at lower pir vales and low values, the strategy should still be considered by policymakers during the initial part of the epidemic to ensure the majority if not all cases are captured at healthcare facilities. nosocomial transmission should also be prevented through the isolation of these cases at the point of admission during testing with the costs accounted for. the prevention of 200-300 covid-19 infections in a hospital at an of 2.5 and incubation period (ip) of 4 days can also prevent transmission within the community and relieve the need for ppe resources which are already under strain. 32 the branching process shows the rapidity of infection spread and highlights the urgency of enhancing hospital surveillance to detect any potential transmission chains when a case is identified, which is already carried out for all atypical pneumonias, some upper respiratory illnesses and hospitalized acute respiratory illnesses. 31 our findings are relevant to cities and highly urbanized regions with well-developed healthcare infrastructure and resources to undertake considerable epidemiological investigation for suspected cases. the costs for areas with fewer resources or different health systems however are likely to be considerably lower but potentially at the cost of a lower pir. a total of 40 000 cases have been confirmed in singapore to date (25th march 2020; a full case listing is provided by gov.sg 33 ) with limited local transmission currently suspected. elsewhere, ~8 million cases and over 435 000 deaths have been confirmed across 6 who regions. 34 the analysis performed here can be utilised for all countries regardless of outbreak stage as it can prevent nosocomial transmission at hospitals with incoming cases of local transmission and prevent imported cases from establishing transmission chains altogether. it also supports the general body of literature highlighting the importance of a highly sensitive standardised criteria for case identification in an epidemic involving a new infectious pathogen. for covid-19, this has been particularly challenging as it shares symptoms with many respiratory illnesses, making it difficult for practitioners to distinguish positive cases. similar issues already exist for influenza between national and regional surveillance programmes where most use measured or reported fever with cough and/or sore throat. 35 during the initial wave of the 2009 influenza a h1n1 pandemic in singapore, serological surveillance on 727 patients from june to october 2009 demonstrated that the revised who definition had the highest reported positive predictive value (ppv) in comparison to three others. 36 this variety in case definition across institutions demonstrates the ongoing challenges in place for both diagnosis and surveillance, which can be difficult for practitioners to interpret and implement. for covid-19, complete case finding is being prioritised where possible in singapore as ppv will substantially change with increasing disease prevalence. provided the case definition is highly sensitive, it can continue to be rapidly updated with greater specificity over time as symptom profile data continues to be shared and assessments carried out on missed cases, therefore sensitivity at the initial phases should be greatly prioritised. the model can be used by policy makers to estimate the costs saved using esc within the hospital setting for the ongoing covid-19 pandemic. esc is cost-effective in the long term, especially at higher 0 and pir values, preventing undiagnosed cases from infecting other individuals, which is especially important during the initial outbreak phase or where the epidemic is suppressed from lockdown measures. it should be noted however that there are several limitations in our analysis, primarily due to the ongoing uncertainties regarding the parameters of covid-19 infection profile and differing operational procedures in hospitals. firstly, the pir is currently unknown and the is likely to vary considerably in space and time across singapore. infectiousness will also vary between hcws and patients which may not be fully explained by the branching process. second, the asymptomatic rate has yet to be determined as part of the continually evolving symptomatic profile. 37, 38 third, we only considered the hospital costs for the institution and did not account for the productivity and economic losses from unnecessary isolation or those saved from averting of nosocomial cases. this also includes the excess manpower costs from hcws who are currently working long hours to ensure patient wellbeing. fourth, revisions may be required to make these findings applicable to other countries or cities through adaption of the isolation and testing procedures. lastly, the potential for superspreading events, as witnessed in sars, 39 has not been accounted for as the movement patterns of hcw were not modelled. esc should be implemented in the early phase of an epidemic where local community transmission is suspected or where imported cases are being repeatedly recorded. cost-savings or relatively minor costs are expected to occur whilst reducing the risk of uncontrolled outbreaks occurring in nosocomial settings. this is critical considering the ongoing anxiety and strain on healthcare systems worldwide, which are reflected within the public and impossible to fully quantify 40, 41 . measures such as esc, which can aid national control efforts, should be considered in order to relieve this pressure through the exhaustive testing and isolation of individuals which have good potential to be positive. 18 contributors jtl, bld, lyac designed the experiments, jtl, bld, arc created the models, bld, jtl, lyac, arc, alk, yyd, daf, pat interpreted the results, bld, jtl, lyac, arc wrote the manuscript, alk and lyac performed data collection for the models. singapore population health improvement centre (nmrc/cg/c026/2017_nuhs) to bld and arc. clinician scientist award (csa) funded by the national medical research council to lyac. ethical approval was not required incubation period 4-8 days lauer 26 linton 27 [20] [21] [22] [23] [24] [25] all costs are rounded to the nearest ten is greater than 10, nearest hundred if greater than 100, thousand if greater than 10 000, and hundred thousand if greater than a million. costs are also in usd. an interactive web-based dashboard to track covid-19 in real time surveillance case definitions for human infection with novel coronavirus clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china clinical characteristics of coronavirus disease 2019 in china sars 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infections transmission characteristics of mers and sars in the healthcare setting: a comparative study a comparative study of clinical features and outcomes in young and older adults with severe acute respiratory syndrome epidemiological, demographic, and clinical characteristics of 47 cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study predictors of mers-cov infection: a large case control study of patients presenting with ili at a mers-cov referral hospital in saudi arabia comparative study of patients with and without sars who fulfilled the who sars case definition the incubation period of covid-19 from publicly reported confirmed cases | annals of internal medicine | american college of physicians incubation period and other epidemiological characteristics of 2019 novel coronavirus infections with right truncation: a statistical analysis of publicly available case data epidemiological and clinical characteristics of 99 cases of 2019 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cardiovascular health care economics indirect costs and cost-effectiveness analysis we declare no competing interest the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.j o u r n a l p r e -p r o o f key: cord-273961-ja8xggnd authors: nakagawara, kensuke; masaki, katsunori; uwamino, yoshifumi; kabata, hiroki; uchida, sho; uno, shunsuke; asakura, takanori; funakoshi, takeru; kanzaki, sho; ishii, makoto; hasegawa, naoki; fukunaga, koichi title: acute onset olfactory/taste disorders are associated with a high viral burden in mild or asymptomatic sars-cov-2 infections date: 2020-07-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.034 sha: doc_id: 273961 cord_uid: ja8xggnd we investigated the association between symptoms and viral clearance in 57 patients with asymptomatic/mild sars-cov-2 infection using cycle threshold (ct) qpcr values. patients with olfactory/taste disorders (otds) exhibited lower qpcr ct values and longer time to negative qpcr than those without otds, suggesting association between otds and high viral burden. severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection has spread globally. in tokyo, japan, the total number of confirmed cases has been increasing, particularly from march to april 2020. real-time polymerase chain reaction (qpcr) using clinical specimens such as nasopharyngeal swabs or sputum is the standard of reference for diagnosis, and recent studies have shown an association between qpcr cycle threshold (ct) values and disease severity (1, 2) . specifically, ct values from qpcr tests conducted on nasopharyngeal or sputum specimens of patients on admission were negatively associated with disease severity and progression to severe illness, and mild patients showed an early viral clearance using ct values (1, 2) . however, little is known about the association between symptoms and viral clearance. our study investigated this association in mild/asymptomatic cases using qpcr ct values of nasopharyngeal swab samples. fifty-seven patients with asymptomatic/mild sars-cov-2 infection (without pneumonia or any organ failure), who were admitted to keio university hospital for isolation and/or treatment from march 28 to april 23, 2020, were included in this study. all patients had no symptoms of dyspnea and, no findings of pneumonia on chest x-ray on admission. they were diagnosed with sars-cov-2 infection using qpcr conducted upon admission and did not receive any antiviral treatments. pre-admission symptoms were collected at admission, and after admission, patients were prospectively checked daily by physicians for symptoms, such as fever, sore throat, nasal drip/congestion, cough/sputum, olfactory and taste disorders (otds), headache, fatigue, joint pain, and diarrhea. qpcr was performed on all nasopharyngeal swab samples using the sars-cov-2 cdc assay protocol and ct values were reported for two genetic markers, the n1 and n2 viral nucleocapsid protein gene regions j o u r n a l p r e -p r o o f (3) . a value of 45 cycles or less indicates a positive result for sars-cov-2. qpcr testing was repeated every 3-7 days until the results were negative. we retrospectively assessed the association between symptoms and ct values or the period to negative qpcr. the clinical characteristics and symptoms of the patients are shown in appendix 1. the mean age was 35.4 years and 25 patients (43.9%) were males. thirty-four patients (59.6%) had comorbidities (all under control). the most common disease was neoplasia (12.3%), followed by asthma (8.8%), and psychiatric disorders (7.0%). twenty-eight patients (49.1%) were asymptomatic, with common symptoms on clinical courses being fever (15; 26.3%), sore throat (11; 19.3%), acute onset otds (10; 17.5%), headache (7; 12.3%), cough/sputum (8; 14.0%), and nasal drip/congestion (4; 7.0%). figure 1 shows the prevalence of each symptom over time. fever, sore throat, and nasal drip congestion were relatively early and prolonged for about one week. the median duration of fever was 3 days (interquartile range: our results showed that patients with asymptomatic or mild sars-cov-2 infection with a higher viral load required a longer time to exhibit negative qpcr results, suggesting that ct values reflect viral load in principle (4) . moreover, our results demonstrated that fever and otds were significantly associated with a higher viral burden and longer time to negative qpcr. compared with fever, data on otds are less available unless intentionally assessed, even though otds are a common symptom in sars-cov-2 infection (5-7). immune genes. nat med 2020;26:681-7. https://doi.org/10.1038/s41591-020-0868-6. hou viral dynamics in mild and severe cases of covid-19 sars-cov-2 viral load in sputum correlates with risk of covid-19 progression centers for disease control and prevention. 2019-novel coronavirus (2019ncov) real-time rrt-pcr panel primers and probes cov-2 infections and transmission in a skilled nursing facility olfactory dysfunction: a highly prevalent symptom of covid-19 with public health significance acute-onset smell and taste disorders in the context of covid-19: a pilot multicentre polymerase chain reaction based case-control study self-reported olfactory and taste disorders in sars-cov-2 patients: a cross-sectional study cov-2 entry factors are highly expressed in nasal epithelial cells together with innate key: cord-024631-yvek5vjz authors: althaus, t.; thaipadungpanit, j.; greer, r.c; swe, m.m.m; dittrich, s.; peerawaranun, p.; smit, p.w; wangrangsimakul, t.; blacksell, s.; winchell, j.m.; diaz, m.h.; day, n.p.j; smithuis, f.; turner, p.; lubell, y. title: causes of fever in primary care in southeast asia and the performance of c-reactive protein in discriminating bacterial from viral pathogens date: 2020-05-11 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.016 sha: doc_id: 24631 cord_uid: yvek5vjz objectives: we investigated causes of fever in the primary levels of care in southeast asia, and evaluated whether c-reactive protein (crp) could distinguish bacterial from viral pathogens. methods: blood and nasopharyngeal swab specimens were taken from children and adults with fever (>37.5˚c) or history of fever (<14 days) in thailand and myanmar. results: of 773 patients with at least one blood or nasopharyngeal swab specimen collected, 227 (29.4%) had a target organism detected. influenza virus type a was detected in 85/227 cases (37.5%), followed by dengue virus (30 cases, 13.2%), respiratory syncytial virus (24 cases, 10.6%) and leptospira spp. (9 cases, 4.0%). clinical outcome was similar between patients with a bacterial or a viral organism, regardless of antibiotic prescription. crp was higher among patients with a bacterial organism compared to those with a viral organism (median 18 mg/l, interquartile range [10-49] versus 10 mg/l [≤8-22], p-value 0.003), with an area under the curve of 0.65, 95% confidence interval (0.55-0.75). conclusions: serious bacterial infections requiring antibiotics are exceptions rather than the rule in the first lines of care. crp-testing could assist in ruling out such cases in settings where diagnostic uncertainty is high and routine antibiotic prescription is common. the original crp randomised-controlled trial (rct) was registered with clinicaltrials.gov, number nct02758821. fever is a common reason for seeking healthcare in southeast asia and as malaria incidence declines, bacteria and viruses now represent the main contributors to acute febrile illness [1] [2] [3] [4] [5] . identifying these pathogens is challenging, even in well-resourced laboratories with specialised staff, and most aetiological data for febrile illness originate in tertiary hospitals [6] . hospitalised patients, however, are by definition more severely ill, often with important comorbidities, implying that findings may not be applicable to febrile patients attending primary levels of care. primary care in low-middle income countries (lmics) is typically characterised by a shortage in human resources, diagnostics and evidence-based guidelines [7] . studies investigating causes of fever in this environment are few and frequently of poor quality: enrolment is often limited to a single clinical presentation and specific age category, and microbiological investigations rarely use goldstandard methods [8] [9] [10] . additionally, most primary care patients attend early after symptom onset with non-severe presentations, lowering the chances of detecting a pathogen [8] [9] [10] [11] [12] [13] [14] [15] [16] . empiric treatment guidelines are therefore based on limited epidemiological evidence and are often implemented by insufficient and poorly trained staff, contributing to irrational antibiotic prescription practices [17] [18] [19] . high prescription levels are partly driven by frequent clinical overlap between bacterial and viral infections, challenging the identification of patients who might benefit from antibiotics [2, 3, 20] . given these limitations in clinical judgment and laboratory structures, point-of-care testing (poct) to guide fever management could be beneficial in primary care settings [21] . pathogen-specific tests represent one such option but several barriers undermine their potential use: these only exist for a small number of pathogens, with inconsistent performance, and most are antibody detection-based that might preclude the distinction between active infection and past-exposure [22, 23] . a few antigen detection-based pocts exist but their integration in low-level care is unrealistic: a salmonella typhi rapid test requires laboratory infrastructure with poor detection in blood even at high concentrations and results are not available before 24-48 hours [24, 25] ; test sensitivities for influenza virus a, respiratory syncytial virus (rsv) and group a streptococcus antigen-based pocts are inconsistent j o u r n a l p r e -p r o o f 5 [26] [27] [28] [29] ; and accurate dengue antigen-based rdts have not been found to be cost-effective in resource-poor settings [30, 31] . non-specific host biomarkers measure the host-response to stimuli, and have been evaluated in the context of fever to discriminate between bacterial and viral pathogens [32] . c-reactive protein (crp) is one of the most studied host-response biomarkers of bacterial infection, consistently showing high sensitivity and moderate specificity, and crp pocts have been shown to be cost-effective in resource-poor environments [30, 32] . however, 80% studies evaluating crp performance originate from high income countries [32] . in southeast asia, these evaluations are mainly hospital-based [33] [34] [35] other than a single community-based study [36] . good diagnostic performance of crp in identifying bacterial infections was observed but generalisability was limited due to demographic, clinical and diagnostic heterogeneity of these studies. in this study, we aim to identify key organisms among acutely febrile children and adults attending primary health care in southeast asia, and to evaluate the performance of crp for discriminating between bacteria and viruses. chiang rai province is the northernmost province in thailand bordering myanmar and lao people's democratic republic. the majority of the population are thai, with approximately 15% ethnic minorities and hill-tribes. the six participating primary care sites were located within a 30-kilometre radius of chiang rai city centre, covering rural and peri-urban as well as mountainous and plateau areas. hlaing tha yar, lower myanmar, is a peri-urban township on the west side of yangon. the township has the highest rates of diseases related to hygiene and environmental conditions (e.g. diarrhoea, dysentery, and tuberculosis) in yangon [37] . four sites were included: three primary care clinics and one outpatient department from a public governmental hospital. both chiang rai and hlaing tha yar are defined by a tropical climate. specimens were collected from febrile patients recruited into a previously described multi-centre randomised-controlled trial evaluating the impact of c-reactive protein (crp) testing on antibiotic prescription in primary care [38] . febrile children and adults (defined as ≥12 years of age) were recruited between june 2016 and august 2017. inclusion criteria were age ≥1 year with a documented fever (defined as a tympanic temperature >37.5˚c) or a chief complaint of acute fever (<14 days), regardless of previous antibiotic intake and co-morbidities other than malignancies. exclusion criteria were symptoms requiring hospital referral defined as either impaired consciousness; inability to take oral medication or convulsions; a positive malaria test; the main complaint being trauma and/or injury; suspicion of either tuberculosis, urinary tract infection, local skin infection or dental abscess; any symptom present for more than 14 days; any bleeding; and inability to comply with the follow-up visit at day 5. on the day of enrolment, all patients had demographic information collected and underwent a routine clinical examination including vital signs (blood pressure, pulse, respiratory rate, temperature). patients were followed-up after their enrolment both at day 5 and day 14. of the 2,392 febrile children and adults recruited, 799 were randomly allocated to the control group with blood specimens collected for off-site crp testing (as compared with the intervention groups that had crp tests performed on-site). details are illustrated in figure 1 . antibiotics were prescribed to this group according to routine clinical practice, clinicians were not informed of the crp results or any aetiological findings. in case of co-detection in blood and np swabs, target organisms detected in blood were assumed to be the primary cause of illness. bacterial and viral aetiological groups included all cases where any bacteria or viruses were detected in blood, respectively, and only target viruses and bacteria detected in np swabs. we described organism distribution among children and adults (defined as ≥12 years of age) separately. descriptive analysis for continuous variables with normal distribution used means and standard deviations (sd) and medians with inter-quartile ranges (iqr) for non-normally distributed continuous variables. comparison between groups used t-tests for normally distributed variables, the mann-whitney test for non-normally distributed variables, and chi-squared test for categorical variables. crp values were compared across aetiological groups and clinical syndrome using the mann-whitney u test for two-group comparisons and the kruskal-wallis test for multi-group comparisons. non-parametric receiver operating characteristic (roc) curves were plotted and the wald test was used to compare areas under the curve. covariates included the following factors: patient age and prior use of antibiotics. diagnostic accuracy was assessed by calculating the areas under the roc j o u r n a l p r e -p r o o f 9 curves (auc). an auc of >0.9 was considered excellent; 0.8-0.9, very good; 0.7-0.8, good; 0.6-0.7, average; <0.6, poor [39, 40] . sensitivity, specificity, and percentage of correctly classified cases were also assessed for the two crp cut-off points used in the original trial: 20 mg/l and 40 mg/l and these were compared with the accuracy of routine prescribing practice [38] . data analyses were performed with stata version 15 (college station, texas, usa). the protocol, informed consent form and case record forms were reviewed and approved by the of the 799 patients prospectively enrolled and randomised into the trial control group, 773 (96.8%) had at least one blood or np swab specimen collected, including 371 (48.0%) children and 402 adults (52.0%). out of these 773 patients, 33 had only a np swab and no blood collected, while 146 had only a blood specimen collected without a np swab. among these 146 patients, 80 had a blood specimen obtained on a dried blood spot (dbs). as shown in table 2 , children presented significantly earlier after symptom onset than adults, with fewer comorbidities and less self-reported medication (p <0.05). antibiotic intake declaration was similar in children and adults (p = 0.237). page 10 of 31 j o u r n a l p r e -p r o o f 10 clinically, respiratory syndrome was the most prevalent presentation both in children and adults. within patients with a respiratory syndrome, the most frequent symptoms were localised in the upper respiratory tract including common cold, diagnosed in 48.2% (120/249) of children and 45.0% (108/240) of adults (p = 0.479). gastrointestinal syndrome was the second most prevalent presentation, and there were no differences between children and adults. 630 blood specimens tested for bacterial screening, using taqman array card (n=601) and bacterial singleplex polymerase chain reaction (n=626) ** 634 blood specimens tested for leptospira screening, using the taqman array card (n=601), the bacterial singleplex polymerase chain reaction (n=626) and the microagglutination test (n=134) *** 658 blood specimens tested for orientia tsutsugamushi and rickettsia spp. screening, using taqman array card (n=601), the bacterial singleplex polymerase chain reaction (n=626), and the indirect immmunofluoresence assay (n=656) **** 601 blood specimens tested using the taqman array card only (n=601) ***** 686 blood specimens tested for dengue, chikungunya and zika virus screening, using taqman array card (n=601), the viral singleplex polymerase chain reaction on fresh blood (n=626) and dried blood spot (n=245) no evidence for a difference in antibiotic prescription was observed between the bacterial and viral groups at day 0, and clinical outcomes were also not significantly different between the two groups (table 4 ). outcome characteristics by aetiological group in chiang rai, northern thailand and hlaing tha yar, lower myanmar, 2016-2017. the prescription of antibiotics at the facility was considered between the enrolment at day 0 until day 14 of the follow-up severity was ranked from 1-4 with severity=1 as the less severe presentation crp: c-reactive protein elevated crp defined as ≥50 mg/l in children and ≥100 mg/l in adults sae: serious adverse event, defined as admission to hospital or death within 14 days of enrolment broad-spectrum antibiotics include ceftriaxone, cefixime, ciprofloxacin, levofloxacin, azithromycin, and amoxicillin with clavulanic acid. among patients with a bacterial organism, two-thirds did not receive any antibiotic ( occurrence of sae, n (%) 0 (0) 0 (0) 1.000 unscheduled visits, n (%) 0 (0) 6 (3.1) 0.281 antibiotic. no evidence for a difference in clinical outcomes was observed after 14 days of follow-up, regardless of whether an antibiotic was prescribed. of we investigated the spectrum of organisms among febrile children and adults in the community and evaluated the performance of crp in distinguishing bacteria from viruses including its potential impact on antibiotic prescription compared with current practice. patients were recruited prospectively across ten sites in thailand and myanmar including urban, semi-urban and rural areas spanning over a full calendar year. in our study, leptospira spp., influenza virus and dengue virus were the leading organisms identified, which is consistent with previous reports in the region [8, 36] . the broad inclusion criteria, allowing for enrolment of all patients over 1 year old regardless of previous antibiotic intake, comorbidities, or clinical presentation, make our findings more generalisable than previous studies. investigating non-malarial acute febrile illness remains challenging in resource-poor areas [8] , and despite screening for multiple organisms on blood and respiratory specimens, we were only able to identify a probable cause of fever in 227 (29.4%) of patients. this low detection may be explained by the inclusion of only non-severe outpatients [14, 41, 42] , while other studies in southeast asia recruiting more severe and hospitalised patients identified an organism in around 50% of cases [2] [3] [4] 35] . only 15.9% (36/227) of organisms detected were bacteria, which may be explained by the lower risk of bacterial infections in non-severely ill patients, and where present, characterised by lower bacterial loads [42] . most bacteria were identified using a singleplex pcr and not the tac assay, while viruses were equally detected by these two molecular methods. this lower sensitivity in the tac assay for the detection of bacteria has been described in previous studies using multi-pathogen molecular detection platforms [43, 44] . the trade-off between advantages for screening multiple organisms at the same time with a simplified molecular platform should be weighed against potentially lower sensitivity, especially for bacteria such as o. tsutsugamushi or leptospira spp., which are considered important drivers of acute febrile illness in southeast asia [45, 46] . the tac assay to identify infections among neonates in south asia, but detected the presence of certain organisms among both controls and cases [47] . a 2019 multi-country study into causes of severe pneumonia also excluded molecular assay results positive for k. pneumoniae because of poor assay specificity [48] . furthermore, most of our patients presented with low crp regardless of whether a bacterial or viral organism was detected, and recovered regardless of whether an antibiotic was prescribed. it is likely that invasive bacterial infections requiring an antibiotic are exceptions while most primary care patients present with a self-limiting infection [49] . other primary care-based studies have recently supported restriction of antibiotic prescription to a small minority of patients: in tanzania, a clinical trial using a 80 mg/l threshold lowered antibiotic reduction to 2.3% without affecting outcomes, while a u.s. study concluded that 72% of outpatients attending a general practice for a respiratory presentation should not even require a medical consultation, let alone an antibiotic prescription [50, 51] . strategies whereby testing for crp as a predictor of clinical outcome rather than determining aetiology have been evaluated in primary care: a cluster-randomised controlled trial in belgium showed crp to rule-out serious infection using a 5 mg/l threshold, while a systematic review found crp-testing to be useful in identifying serious infections among febrile children [52, 53] . in our study, crp performance in distinguishing bacteria from viruses was average (auc 0.65) and lower than another study from the region which found (auc 0.83 among 1,372 patients with a microbiologically-confirmed diagnosis from thailand, cambodia and lao pdr [36] our study has several limitations, mostly relating to the limited scope and accuracy of the reference diagnostic tests, and the impact of even slightly less than perfect "gold-standard" reference tests on the evaluation of new diagnostic and biomarker tests can be profound [56, 57] . as mentioned above, the sensitivity and specificity of the multiplex tac assay was not optimal for bacteria detection, and the absence of convalescence specimens impeded our ability to diagnose patients based on serology, particularly with respect to bacterial zoonoses. even genuine detection of bacterial and viral dna in normally sterile sites cannot be used to conclusively determine causality, as this has been reported among healthy individuals, and in patients even weeks after recovery from infections, challenging the interpretation of molecular assays [58, 59] . blood culture was not available and this further limited our aetiological investigation. we did not recruit a concomitant control group, which precludes robust attribution of causality in the organisms we detected, particularly in np swabs. in a paediatric study in asia and africa, the inclusion of controls matched with pneumonia cases weakened the evidence of causality for almost all organisms detected [48] , and only rsv, hmpv, influenza virus a and b, parainfluenza virus type 1 and b. pertussis were considered pathogenic, consistent with other lmicbased studies [60, 61] . these organisms, however, are sometimes present in healthy individuals, with a prevalence of influenza virus among healthy children between 0-6%, rsv at 0-9% and hmpv between 0-7% [62] . on the other hand, we did not regard other organisms detected in np swabs such as rhinovirus, parainfluenza virus or s. pneumoniae as pathogenic, because these are commonly detected among healthy individuals [48, 63, 64] . all these limitations in reference diagnostic tests might explain the average performance of crp in our analysis. we presented the key organisms detected among febrile children and adults attending primary healthcare in southeast asia. the performance of crp in distinguishing between bacterial and viral organisms was limited, although the current findings suggest that crp-guided treatment would increase the appropriate use of antibiotics with respect to aetiology. this is supported by the overall reduction in prescribing compared with current practice demonstrated in the original trial. our findings also support conclusions from previous studies that even in the presence of bacterial organisms, very few ambulatory patients are likely to benefit from the extensive and poorly targeted antibiotic prescribing practices that currently prevail in most southeast asian primary care settings. the funders had no role in study design, data collection, data interpretation or writing the manuscript. the corresponding author had full access to all the data and took the final decision to submit for publication.  point-of-care diagnostic tools could guide health 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admission in children without hiv infection from africa and asia: the perch multi-country case-control study. the lancet. 2019. 49. van den bruel a safety and efficacy of c-reactive protein-guided antibiotic use to treat acute respiratory infections in tanzanian children: a planned subgroup analysis of a randomized controlled noninferiority trial evaluating a novel electronic clinical decision algorithm (epoct) necessity of office visits for acute respiratory infections in primary care diagnostic value of laboratory tests in identifying serious infections in febrile children: systematic review point-of-care c-reactive protein testing to reduce inappropriate use of antibiotics for non-severe acute respiratory infections in vietnamese primary health care: a randomised controlled trial the effect of uncertainty in patient classification on diagnostic performance estimations imperfect gold standards for biomarker evaluation van der pol b. duration of polymerase chain reaction-detectable dna after treatment of chlamydia trachomatis, neisseria gonorrhoeae, and trichomonas vaginalis infections in women. sexually transmitted diseases detection of the latent form of epstein-barr virus dna in the peripheral blood of healthy individuals microorganisms associated with pneumonia in children< 5 years of age in developing and emerging countries: the gabriel pneumonia multicenter, prospective, case-control study the role of influenza, rsv and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high hiv sero-prevalence viral and bacterial interactions in the upper respiratory tract frequent detection of respiratory viruses without symptoms: toward defining clinically relevant cutoff values asymptomatic shedding of respiratory virus among an ambulatory population across seasons. msphere we thank all primary care patients and health workers from chiang rai primary care centres and hlaing tha yar public hospital and mam clinics for taking part in the study. we are very grateful to the study staff and to the clinical trial support group at mahidol-oxford tropical medicineresearch unit for ensuring the successful completion of the study. we thank heiman wertheim, arjen dondorp, direk limmathurotsakul, christopher parry, and paul newton for guidance on the study design; clare ling, toni whistler, ampai tanganuchitcharncha, areerat thaiprakhong, nattapon pinthong, prapaporn srilohasin and kyaw soe for laboratory support, as well as duangjai suwancharoen from the national institute for animal health (niah) for carrying out the leptospira mat. finally, we thank elizabeth ashley, jeroen bok, joshua cohen, ni ni tun, and khin yupar soe for their assistance in study site coordination. key: cord-287209-hkrarxsd authors: zhao, shi; lin, qianyin; ran, jinjun; musa, salihu s; yang, guangpu; wang, weiming; lou, yijun; gao, daozhou; yang, lin; he, daihai; wang, maggie h title: the basic reproduction number of novel coronavirus (2019-ncov) estimation based on exponential growth in the early outbreak in china from 2019 to 2020: a reply to dhungana date: 2020-02-20 journal: int j infect dis doi: 10.1016/j.ijid.2020.02.025 sha: doc_id: 287209 cord_uid: hkrarxsd nan to the editor the ongoing outbreak of the novel coronavirus (2019-ncov) pneumonia in wuhan, china and other regions remains a major public health concern. we thank dhungana's comments to our study, zhao et al. [1] , recently published in the international journal of infectious diseases. the estimates on the basic reproduction number, r0, were carried out in early outbreak as of january 22, 2020 when the surveillance data and the knowledge on the key epidemiological features of 2019-ncov were limited. the assumptions of exponential growth as well as other similar growing patterns are commonly accepted and adopted to capture the growing trends during the early phase of an outbreak [2] [3] [4] . the exponential growing rate (γ), or the intrinsic growing rate, is estimated from the early epidemic curve and used to calculate the r0. we repeat the analysis in zhao et al. [1] , γ is estimated at 0.18 (95%ci: 0.14−0.22), 0.15 (95%ci: 0.12−0.18) and 0.11 (95%ci: 0.09−0.13) per day associated with 2-, 4-and 8-fold increase in the reporting rate, respectively. by using the serial interval (si) estimate (mean ± sd at 7.5 ± 3.4 days) from li et al. [5] , we found the r0 at 3.33 (95%ci: 2.17−4.04), 2.69 (95%ci: 2.28−3.17) and 2.13 (95%ci: 1.88−2.42) associated with 2-, 4-and 8-fold increase in the reporting respectively. our estimates were in line with the who estimates in both early version (2-fold case) and the published version. the key message as we highlighted in the paper is the changes in reporting rate. this is recently reconfirmed by tuite and fishman [6] . we thank the editor and dhungana to give us this opportunity to reclarify our key message that the reporting rate was not constant during the early outbreak and could affect the estimation of r0. there is indeed a large amount of later confirmed cases which were not counted in the early official daily situation reports [5, [7] [8] [9] . in other words, if the same reporting standard in the second half of january was applied to the first half of january, the number of cases would be much higher. other teams either used retrospective dataset which was not publicly available on january 23, 2020 or used oversea reported cases which was not (to a much less extent) affected by the changes in reporting rate. by using the same analysis and dataset as in zhao et al. [1] , an additional sensitivity analysis on the r0 estimates and varying si and reporting rate was conducted and shown in fig 1. we report that r0 estimates increase while the mean of si increases or the sd of si decreases. by selecting mean between 7 and 8 days and sd between 3 and 4 days for si of 2019-ncov, the r0 estimates are largely consistent within a range from 2 to 4 in many existing literatures [5, [7] [8] [9] [10] , see panels (f), (g), (j) and (k) fig 1. we conclude that our previous estimation and main conclusions in [1] hold based on the reasonable selection of the si estimates of 2019-ncov. not only our early version (2-fold case) is in line with the who estimates, but also we pointed out the issue in the reporting rate changes in the official reported cases. the estimates of the basic reproduction number, r0, with varying reporting rates, mean and sd of serial interval (si). the mean of si, from top to bottom vertically, varies at 6, 7, 8 and 9 days. the sd of si, from left to right horizontally, varies at 2, 3, 4 and 5 days. the light-yellow area highlights the r0 ranging from 2 to 4 referring to the estimates in [5, [7] [8] [9] [10] . the blue bold curve is the mean estimate, and the blue dashed curves are the 95% confidence interval (95%ci). preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak early transmission dynamics of ebola virus disease (evd) the basic reproductive number of ebola and the effects of public health measures: the cases of congo and uganda appropriate models for the management of infectious diseases early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia reporting, epidemic growth, and reproduction numbers for the 2019 novel coronavirus (2019-ncov) epidemic. annals of internal medicine estimating the potential total number of novel -ncov) cases in wuhan city, china. preprint published by the imperial college pattern of early human-to-human transmission of wuhan estimating the unreported number of novel coronavirus (2019-ncov) cases in china in the first half of january 2020: a data-driven modelling analysis of the early outbreak nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study the authors thank cindy y tian from the chinese university of hong kong for helping on processing the reference files.j o u r n a l p r e -p r o o f the authors declared no competing interests. all authors conceived the study, carried out the analysis, discussed the results, drafted the first manuscript, critically read and revised the manuscript, and gave final approval for publication. key: cord-268389-0agwvsrv authors: kaminski, monica a.; sunny, subin; balabayova, khayala; kaur, avneet; gupta, aanchal; abdallah, marie; quale, john title: tocilizumab therapy of covid-19: a comparison of subcutaneous and intravenous therapies date: 2020-09-28 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1447 sha: doc_id: 268389 cord_uid: 0agwvsrv background the release of pro-inflammatory cytokines, resulting in cytokine storm syndrome, contributes to the morbidity and mortality associated with covid-19 disease. this study aimed to compare the effects of intravenous (iv) and subcutaneous (sc) tocilizumab, an il-6 receptor antagonist, on respiratory parameters and clinical outcome in patients with covid 19. methods we performed a retrospective cohort study of hospitalized patients with covid-19 treated with either iv or sc tocilizumab from march 26, 2020 to may 18, 2020. respiratory parameters seven days after receiving tocilizumab therapy were compared to baseline measurements. all patients were assessed until discharged from the hospital. results tocilizumab was administered to 125 patients: 65 received iv and 60 received sc therapy. at day seven, 52% of the patients in the iv group demonstrated improvement in respiratory parameters, compared to 28% in the sc group (p = 0.01). mortality rates at days seven and 28 were 15% and 37%, respectively in the iv group and 17% and 50%, respectively in the sc group (p = ns). in-hospital mortality rate was 38% for the iv group versus 57% for the sc group (p = 0.04). more than 90% of patients in each group received corticosteroids, however significantly more patients in received convalescent plasma in the iv group. conclusions at the doses used in this study, iv tocilizumab is preferred over sc therapy for the treatment of cytokine storm syndrome due to covid-19. the novel coronavirus, sars-cov-2, emerged in wuhan, china in december 2019, and spread rapidly around the globe causing covid-19 disease. as of july 2020, there have been 10 million j o u r n a l p r e -p r o o f cases reported, with 500,000 fatalities (https://www.who.int/emergencies/ diseases/novelcoronavirus-2019/situation-reports). while the majority of covid-19 cases are mild and selflimiting, severe disease and death can occur. risk factors for progression to critical illness and death include advanced age, underlying cardiac or renal disease, and obesity (wu et al. 2020 , petrillo et al. 2020 ). progressive illness is characterized by massive alveolar damage, progressive respiratory failure, and multi-organ dysfunction (xu z et al. 2020 , chen n et al. 2020 . post-mortem analyses have shown an overactivation of th17 and cd8 t cells with release of proinflammatory cytokines resulting in immune injury and cytokine storm. interleukin-6 (il-6) is a pro-inflammatory cytokine that has been shown to be elevated in patients with severe disease (chakraborty et al. 2020 , luo et al. 2020 , alghari et al. 2020 , and a potential target to reduce disease progression. tocilizumab is a recombinant humanized monoclonal antibody that is directed specifically against the interleukin-6 receptor (il-6r) and works by binding to both soluble and membrane-bound il-6r, resulting in inhibition of il-6-mediated signaling through these receptors (le et al. 2018 , antwi-amoabeng et al. 2020 . tocilizumab is fda approved for use in patients with rheumatoid arthritis, systemic juvenile idiopathic arthritis, giant cell arteritis, and lifethreatening cytokine release syndrome associated with the use of chimeric antigen receptor t-cells. several studies have documented favorable outcomes following tocilizumab therapy in patients with severe covid-19 disease. xu et al reported the use of tocilizumab (administered as a one-time 400mg intravenous dose) in 21 patients with covid-19 that resulted in no deaths, with 90% of their patients discharged home (xu x et al., 2020) . subsequent studies have also demonstrated benefit, with reductions in overall mortality, particularly in patients with more advanced disease (requiring mechanical ventilation) (toniati et al., 2020 , klopfenstein et al. 2020 , rossotti et al., 2020 , somers et al., 2020 , guaraldi et al., 2020 . however, not all reports have been so favorable, especially in j o u r n a l p r e -p r o o f critically ill patients (luo et al., 2020) . in addition, adverse effects (including superinfections and prolongation of hospital stay) have been noted (rossotti et al., 2020 , somers et al., 2020 , guaraldi et al., 2020 . both intravenous (iv) and subcutaneous (sc) formulations of tocilizumab have been used to treat the cytokine storm due to covid-19, with apparent equal effect (guaraldi et al., 2020) . it is noteworthy that the pharmacokinetic profiles of the two formulations differ greatly. sc injection has an absorption half-life of approximately 4 days, resulting in a delayed achievement of cmax (tocilizumab package insert, 2017). in patients with rheumatoid arthritis, administration of 162 mg tocilizumab sc weekly and biweekly resulted in maximum serum levels of 9.3 ± 5.1 µg/ml and 5.8 ± 4.1 µg/ml, respectively (lee et al., 2014) . in contrast, 8mg/kg of tocilizumab given iv weekly resulted in a maximum serum concentration of 136 ± 34 µg/ml (lee et al., 2014) . whether a more delayed but sustained effect following sc administration, or a more intensive but shorter-lived effect following iv administration, is preferable in managing cytokine storm is unknown. in this report, the respiratory and clinical outcomes of patients treated with either iv or sc tocilizumab therapy for covid-19 are compared. consecutive patients receiving tocilizumab for covid-19 related illness between march 26,2020 through may 18, 2020 underwent standardized chart review. our medical center, a large tertiary care facility located in brooklyn, serves a predominantly minority and underserved population. all admitted patients with suspected or proven covid-19 illness who were in respiratory distress (typically defined as a peripheral oxygen saturation ≤ 93 % on room air) were considered eligible for tocilizumab therapy. standard of care treatment developed at our institution included hydroxychloroquine 400 mg twice a day for one day followed by 200mg twice a day for an additional 4 days plus azithromycin 500mg once followed by 250mg oral once daily for an additional 4 days. concomitant with tocilizumab therapy, short courses (typically 3-5 days) of corticosteroids were encouraged; corticosteroid dosing was often left to the discretion of the primary care providers. tocilizumab was administered at 400 mg iv, typically as single dose, based on initial reports (xu x et al., 2020) . when the intravenous formulation was unavailable, the subcutaneous formulation was used. at our institution, a decision to use a sc dose of 324 mg (given as two simultaneous doses of 162 mg) was based on known pharmacokinetic data (zhang et al., 2013) . it should be noted this was the same dosage used in another comparator study (guaraldi et al., 2020) . the study was approved by the institutional review board at suny-downstate medical center and the system to track and approve research at nyc health and hospitals. patients treated with tocilizumab were retrospectively identified by review of pharmacy records. for each patient, a subsequent review of the electronic medical record was performed to obtain demographic, clinical, and laboratory information. the respiratory parameters for the 24 hours preceding the dose of tocilizumab and on days three and seven post-administration were recorded. two respiratory-based criteria were used to assess response to tocilizumab therapy: 1) to detect subtle changes in respiratory parameters, definitions of ventilatory response were taken to mirror national healthcare safety network (nhsn) definitions for ventilatory-associated events. for each 24-hour period under review, the highest levels of oxygen requirement (i.e., fio2) or peep that were sustained for at least one hour were recorded. patients were considered to have ventilatory improvement if there was a decrease in fio2 of ≥ 20% or peep of ≥ 3 cm h2o (with a peep setting of 0-5 cm h2o as the lowest setting). patients were also considered to have responded if there was an incremental decrease in oxygen requirement reflected by a change from a higher to a lower category of oxygen support: mechanical ventilation (highest category), bipap/cpap, high flow nasal canula, low-flow facemask, low flow nasal canula, and room air (lowest category). 2) to determine more overt changes in respiratory parameters at day 7, the disease severity scale employed by li et al., 2020 was used. this ordinal scale consists of six clinical points: 6= death; 5= hospitalization with mechanical ventilation; 4= hospitalization with non-invasive ventilation or high-flow oxygen therapy; 3= hospitalization with other oxygen therapy; 2= hospitalization without oxygen therapy; and 1= discharged or achieved discharge criteria. improvement was defined as a reduction by at least two points in the disease severity scale. the following additional clinical information was recorded: 1) prior history of diabetes mellitus, hypertension, and ischemic heart disease; 2) receipt of corticosteroids and convalescent plasma during the 7-day observation period; and 3) duration of symptoms prior to tocilizumab administration. the following inflammatory markers prior to and within seven days post tocilizumab therapy were collected: c-reactive protein, d-dimers, ferritin, il-6, lactate dehydrogenase, and procalcitonin. changes in basic laboratory values and positive cultures of blood were also noted during the 7-day observation period. cytokine release syndrome grades were determined according to the criteria of lee et al., 2018 . as of july 15, 2020, all patients had been discharged from the acute care medical service. survival data was calculated from the day of tocilizumab administration to either death or discharge from the hospital. the primary endpoints were changes in ventilatory status at days three and seven following tocilizumab therapy. secondary endpoints were survival rates at days seven, 28 and during the hospital stay. fisher's exact test and student's t-test were used to compare categorical and continuous values, respectively, between groups. student's t-test for paired values was used to compare pre-and posttocilizumab laboratory values. survival curves were created using the kaplan-meier method and compared using the log-rank test. a p value of ≤ 0.05 was considered significant. there were 125 patients included in the study; 65 received iv and 60 received sc tocilizumab. overall, 87 (70%) patients were african american persons. a nasopharyngeal swab was positive by rt-pcr for sars-cov-2 in 117 patients, with the remaining eight patients highly suspected of having covid-19 illness. overall, 82 patients were receiving supplemental oxygen and/or considered to have severe disease, and 43 were on mechanical ventilation and considered to have critical illness. the baseline characteristics were generally comparable between the patients in the iv and sc groups (table 1) ; there tended to be more females that received iv tocilizumab. at the time of iv tocilizumab therapy, 36 (55%) patients met grade 3 and 27 (42%) patients met grade 4 cytokine release syndrome criteria. similarly, at the time of sc tocilizumab therapy, 32 (53%) patients met grade 3 and 26 (43%) met grade 4 cytokine release syndrome criteria. several laboratory values have been shown to be predictors of mortality in patients with covid-19 (garcia et al., 2020) , including blood levels of potassium, creatinine, d-dimers, lactate, and p/f ratios. the baseline laboratory values for potassium, creatinine, and d-dimer were similar for the iv and sc groups (table 1) . lactate levels (2.4±1.6 vs. 2.1±1.1 mmol/l) and p/f ratios (148±101 vs. 148±89) were also similar between the iv and sc groups, respectively. the percentage of patients with known j o u r n a l p r e -p r o o f ischemic heart disease, also an indicator of higher mortality (garcia et al., 2020) , was also similar in the iv and sc groups: 5 of 65 (8%) vs. 3 of 60 (5%), respectively. il-6 levels have also been correlated with poor respiratory outcomes (herold et al., 2020; and baseline levels were significantly higher in the group that received iv therapy vs. sc therapy (340 ± 655 vs. 124 ± 157 pg/ml, p=0.04). concomitant use of corticosteroids was high in both groups: 94% in the iv group and 90% in the sc group. however, patients in the iv group tended to receive higher daily doses (≥ 500mg of methylprednisolone or equivalent) of corticosteroids than those in the sc group ( using the six point disease severity scale to assess response to therapy (criterion two), more favorable outcomes at day seven were also noted in the iv group. at day seven, 16 (25%) of patients in the iv group had a two point reduction, compared to 6 (10%) of patients in the sc group (p=0.04). improvements in the cytokine release syndrome grades also favored the patients in the iv therapy group. among the survivors at day seven, the average cytokine release syndrome grade fell from 3.33±0.55 to 2.78±1.23, p=0.0003) for the iv group. at day 7, the average cytokine release syndrome laboratory values were also assessed in the survivors at day seven to determine if there were any differences in possible toxicities related to iv vs. sc tocilizumab therapy. laboratory values at baseline were generally similar to values at day seven for patients in the iv group: white blood cell count (12.8±5.1 vs. 14.7±10.3 k/µl), absolute neutrophil count (10.7±4.6 vs. 12.0±9.5 k/µl), j o u r n a l p r e -p r o o f hemoglobin (11.5±2.3 vs. 11.0±2.2 g/dl), platelets (268±117 vs. 274±121 k/µl) and creatinine 1.85±2.34 vs. 1.51±1.76 mg/l). however, alanine aminotransferase levels did rise significantly at day seven, from 57.6±95 to 107±112 u/l (p<0.001). laboratory values at baseline were all similar those at day seven for patients in the sc group: white blood cell count (13.2±6.4 vs. 13.8±8.5 k/µl), absolute neutrophil count (11.0±5.7 vs. 11.1±7.2 k/µl), hemoglobin (11.9±1.9 vs. 11.1±2.7 g/dl), in an attempt to identify factors that might predict improvement in respiratory parameters at day seven, baseline laboratory data were compared (table 2) between the groups of patients showing and lacking (including death) improvement. c-reactive protein levels were significantly higher in patients in the iv group that did not respond (table 2) lastly, laboratory markers of inflammation were analyzed before and during the seven days following tocilizumab therapy to identify trends that correlated with response involving the respiratory parameters (table 3) . for both responders and non-responders in the iv and sc groups, levels of c-reactive protein fell significantly following therapy (table 3) . il-6 levels rose in all groups, however this reached statistical significance only in the non-responders in the sc group. none of the other markers of inflammation collected within seven days following therapy were significantly different than pre-treatment values. it is becoming increasingly evident that targeting the cytokine storm syndrome in patients with covid-19 related illness can improve outcomes. elevated il-6 levels have been identified as a risk factor for adverse outcomes, including worsening respiratory status and death (rossotti et al., 2020 , ruan et al., 2020 . considerable data has accumulated regarding the use of tocilizumab therapy for patients with serious or critical illness due to covid-19. tocilizumab has been found to be associated with improved outcomes in patients with covid-19 related respiratory disease, particularly for patients with critical illness (i.e., requiring mechanical ventilation) (rossotti et al., 2020 , somers et al., 2020 . in one study, both iv (8mg/kg for two doses) and sc (324mg as a single dose) were found comparable in reducing mortality compared to standard of care (guaraldi et al., 2020) . in this report, we found divergent outcomes in patients administered iv vs. sc tocilizumab. we attempted to identify subtle differences in respiratory parameters during the first week of therapy by including national safety healthcare network criteria of ventilator-associated events. as might be anticipated, given the pharmacokinetic differences of iv and sc tocilizumab, greater improvements in respiratory parameters were observed at three and seven days in the group of patients receiving iv therapy. this improvement in respiratory function subsequently translated into improved clinical outcomes -compared to those patients that received sc therapy, patients that received iv therapy had lower in-hospital mortality. over 90% of the patients in our study concomitantly received short courses of corticosteroids. corticosteroid dosing was higher in the group of patients that received iv tocilizumab, possibly contributing to the differences found with the sc group. however, doses of corticosteroids in both the iv and sc groups typically equaled or exceeded 6 mg of dexamethasone per day, a dose that has been found to be beneficial in reducing mortality in patients with advanced covid-19 disease (recovery collaborative group, 2020). the combination of corticosteroids and tocilizumab may have an additive effect in the treatment of cytokine storm syndrome (ramiro et al., 2020) ; it is possible this effect is observed only with iv tocilizumab therapy. laboratory markers of inflammation are often used in the assessment of patients with covid-19. in addition to il-6, elevated levels of c-reactive protein, d-dimers lactate dehydrogenase, and procalcitonin have been associated with poor prognosis (wu et al., 2020 , ruan et al., 2020 , chen r et al., 2020 , zhou et al., 2020 . in this report, patients that received iv tocilizumab that failed to have an improvement in respiratory parameters had higher levels of c-reactive protein than patients that did improve. it is likely that patients with extremely elevated levels of c-reactive protein may require a more aggressive strategy (e.g., multiple doses of tocilizumab). laboratory markers of inflammation are also often used to gauge clinical response to therapy in patients with covid-19. we did not find trends in markers of inflammation that differentiated patients that did or did not have improvement of respiratory parameters seven days after treatment. in our report, levels of c-reactive protein fell acutely in both patients that did and did not have improvement in respiratory parameters seven days following tocilizumab therapy. a decrease in c-reactive protein levels has been observed following tocilizumab therapy with or without corticosteroids (xu x et al., 2020 , rossotti et al., 2020 . our study has several limitations. in addition to being a single center study, as noted above, corticosteroids were administered to over 90% of our patients. more patients in the iv group received supportive treatment with tocilizumab for covid-19: a systematic review 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key: cord-293247-ltxt2dfv authors: elachola, habida; assiri, abdullah; turkestani, abdual hafiz; sow, samba s.; petersen, eskild; al-tawfiq, jaffar a.; memish, ziad a. title: advancing the global health security agenda in light of the 2015 annual hajj pilgrimage and other mass gatherings date: 2015-10-09 journal: int j infect dis doi: 10.1016/j.ijid.2015.10.003 sha: doc_id: 293247 cord_uid: ltxt2dfv nan in the second week of september 2015, health ministers from across the world converged in seoul, korea for the 2 nd high level deliberations on global health security agenda (ghsa). this was yet another attempt to galvanize a unified response to infectious diseases that threaten global health security. 1, 2 this event coincided with the arrival in saudi arabia of nearly 1.5 million pilgrims from over 180 countries who will participate in the 2015 annual hajj pilgrimage. [2] [3] [4] [5] amidst the ongoing global transmission of three viral infections associated with high morbidity and mortality rates with epidemic potential, the ebola virus (ebov), middle east respiratory syndrome coronavirus (mers-cov) and avian influenza virus a (h5n1). [6] [7] [8] the detection in july 2015 of ebola virus from dead body swab of a 17 year old boy in liberia after the declaration of liberia being ebola free in may 2015, and the detection of ebola virus in the dead body of an elderly woman in sierra leone as the country awaits countdown to being declared ebola free, indicate current knowledge gaps of the natural history and pathogenesis. the recent large outbreak of mers-cov in hospitals in seoul, korea and subsequent spillover to china was unprecedented as the largest outbreak outside the middle east. 9 this event illustrated that unless a high degree of awareness and vigilance with effective surveillance and infection control measures are in place, transmission of mers-cov can occur in the home countries can occur upon return of an infected pilgrim. these are all complex challenges that detection of even one case can overwhelm any health systems and adversely affect the economic security of affected countries. although the comprehensive hajj health care and emergency management system of saudi arabia is well positioned to cope with known types of threats and related case management 10 , they are unlikely to detect any incubating transmissions that occurred among pilgrims that remain asymptomatic during the pilgrims stay in ksa. although current ghsa is yet to specifically highlight mass gathering preparedness as a strategic priority even in countries with high participant contribution to mass gatherings, the 12 global health security agenda action packages and the strategies to minimize the implications of mass gathering on public health are similar. the risk of infectious disease transmission during a mass gathering is the same or even more as the risk of transmission that prevails in any one of the home or host countries of mass gathering participants. during the world health assembly 67, a side event took place to launch the lancet series on mass gathering medicine in may 21, 2014 ( figure 1 ). mass-gatherings are held for various purposes including religious rituals, sports activities, or festivals and therefore the demographics, risks, and the intensity of activities vary. further, the risks are exacerbated during mass gatherings such as the hajj for airborne, droplet, and body fluid-related transmission due to the absence of social distancing among participants; increased susceptibility due to stress, lack of sleep, and changing nutritional factors during peak events; disruption of medications among persons with chronic debilitating diseases; and participation in some of the rituals such as animal sacrifices or the practice of scalp hair shaving practices by self-help groups using unsterile blades rather than in regulated barber shops. given that two-thirds of the emerging diseases are zoonotic, human-animal interaction during some mass gatherings such as the hajj further increases the risk, and saudi arabia imports sacrifice animals from 6 countries. thus, except for vaccine preventable diseases, perfection of disease control strategies in one or few countries alone including in the host country may not offer blanket protection from all types of disease transmission dynamics for epidemic prone disease agents present in any one of the countries. the impact of these challenges on public health during mass gatherings can be minimized by two strategies. first, each of the countries that participate in a mass gathering should have alert systems in place to identify diseases of transmission-potential during a mass gathering, control measures in place to avoid the exportation of such risks, and reduce the participation of individuals at risk increased risk for disease acquisition. for ghsa 1 , this relates to adequate syndromic-and agent-based surveillance, laboratory enhancements, and reporting systems and risk communication managed by adequately trained workforce including one epidemiologist for a population of 200,000. furthermore, countries participating in mass gatherings should have public emergency preparedness in response mode and adequate surge capacity to be able to respond to potential emergencies from participants returning from mass gatherings. existence of a public health emergency operations center with sufficient pool of response manpower and medical countermeasures available will be critical. this can only be functional if relevant a national public health preparedness policies and authorities are in place to coordinate a response with diverse organizational entities such as the ministries of aviation, defense, interior, and health. of note, moving from challenges to disease detection opportunities, it is worth noting that mass gatherings provide an unexploited opportunity as an one-stop surveillance venue to monitor emerging disease threats or existing threats of significance in multiple countries. health examinations and specimen collection is routine for hajj pilgrims prior to departure in their home countries and arrival airports in saudi arabia conduct health screenings. additional surveillance programs using rapid detection tests can be implemented in home and host countries of mass gatherings. furthermore, the hajj emergency health management system operates a network of health facilities with electronic data management systems that can conduct syndromic-and agentbased surveillance on symptomatic individuals who seek care (about 500,000 pilgrims on average during each hajj) (10)deliverables that correspond well with the objectives outlined in the ghsa 1 . in summary, it is imperative that opportunities presented by the ghsa in the first round of 17 countries chosen for immediate implementation by the u.s. government 1 , and future beneficiary countries of the ghsa prioritize and program funding and activities that specifically address mass gathering preparedness in addition to sustained routine activities. we now have the knowledge that the world did not have during the 1957 hajj and influenza transmission. as the search for vaccines and treatment continue for these novel challenges, first and foremost priority for the global community is to minimize the effects of emerging threats during mass gatherings would be to activate public health emergency management capacities before, during and after these mass gatherings of significance. mass gatherings offer opportunities to implement, test, and assess ghsa objectives in its entirety and can contribute significantly to health security of individuals, nations, and the world. global health-global health security agenda mass gatherings medicine and global health security public health. pandemic h1n1 and the 2009 hajj mass gatherings medicine: international cooperation and progress mass gathering and globalization of respiratory pathogens during the 2013 hajj the ebola virus disease outbreak. world health organization mers-the latest threat to global health security centers for disease control and prevention, us department of health and human services hajj: infectious disease surveillance and control key: cord-310691-6danlh8h authors: ma, simin; lai, xiaoquan; chen, zhe; tu, shenghao; qin, kai title: clinical characteristics of critically ill patients co-infected with sars-cov-2 and the influenza virus in wuhan, china date: 2020-05-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.068 sha: doc_id: 310691 cord_uid: 6danlh8h objective: to delineate the clinical characteristics of critically ill covid-19 patients co-infected with influenza. methods: in this study, we included adult patients with laboratory-confirmed covid-19 form tongji hospital (wuhan, china), with or without influenza, and compared their clinical characteristics. results: among 93 patients, 44 died and 49 were discharged. forty-four (47.3%) were infected with influenza virus a and 2 (2.2%) with influenza virus b. twenty-two (50.0%) of the non-survivors and 24 (49.0%) of the survivors were infected with the influenza virus. critically ill covid-19 patients with influenza were more prone to cardiac injury than those without influenza. for the laboratory indicators at admission, white blood cell counts, neutrophil counts, levels of tumor necrosis factor-α, d-dimer value, and proportion of elevated creatinine were higher in non-survivors with influenza than in those without influenza. conclusion: the results showed a high proportion of covid-19 patients were co-infected with influenza in tongji hospital, with no significant difference in the proportion of co-infection between survivors and non-survivors. the critically ill covid-19 patients with influenza exhibited more severe inflammation and organ injury, indicating that co-infection with the influenza virus may induce an earlier and more frequently occurring cytokine storm. the world health organization (who) named the coronavirus disease caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) as 2019 novel coronavirus disease and declared it as a pandemic. similar to the influenza virus, sars-cov-2 is commonly transmitted through respiratory droplets and contact. the world's population is generally susceptible to sars-cov-2 infection. most covid-19 patients show mild influenza-like symptoms, such as fever, cough, and fatigue. however, approximately 5% of patients rapidly progress to acute respiratory distress syndrome (ards), septic shock, and multiple organ failure and are admitted to intensive care units. the covid-19-associated mortality rate in china is approximately 2.3% (guan et al. 2020; novel coronavirus pneumonia emergency response epidemiology team 2020) . to date, no studies have reported on critically ill covid-19 patients who also present with influenza. human cases of influenza in wuhan occur in winter most often (he and tao 2018; wang et al. 2018) , which overlaps the peak of covid-19 in wuhan. we speculated whether co-infection with sars-cov-2 and the influenza virus existed. and if so, the influence of this co-infection on clinical features needs to be investigated. the southern hemisphere is yet to enter its flu season for the year and in many of these countries the incidence of covid-19 is still increasing. meanwhile, many western hemisphere countries are still experiencing covid-19 outbreaks. and a great many countries around the world will be looking to start planning for flu season 2020/21 with many public health experts warning of the need to avoid second peaks of covid-19 during flu season. therefore, answering the above questions is crucial for the formulation of treatment strategies to manage co-infection with sars-cov-2 and the influenza virus. in the present study, we extracted the clinical data for 95 patients j o u r n a l p r e -p r o o f with laboratory-confirmed covid-19 from tongji hospital (wuhan) and discussed the clinical characteristics of critically ill covid-19 patients co-infected with influenza. our results may provide new insights into the treatment and control of co-infection with sars-cov-2 and the influenza virus. the study was conducted among 95 adult patients with laboratory-confirmed covid-19 (including 50 discharged cases and 45 non-survivors) discharged/died in and interleukin-6 [il-6], and respiratory virus-specific igm antibodies), detailed medication, and tests for sars-cov-2 from respiratory tract specimens (including nasopharyngeal swabs, bronchoalveolar lavage fluid, sputum, or bronchial aspiration fluid). specimen collection and lung ct scanning were completed for all patients within 24 hours of admission. a confirmed covid-19 case was defined as a positive result in a rt-pcr assay of nasal and pharyngeal swab specimens according to who guidelines. on receipt of the samples, viral rna extraction was performed using a magnetic viral rna/dna extraction kit (tianlong, xi'an, china) following the manufacturer's instructions. this was followed by pcr screening for the specific detection of sars-cov-2 using a commercial kit (tianlong). a cycle threshold value (ct-value) ≤37 was defined as a positive test based on the recommendation of the national institute for viral disease control and prevention (china). statistical analysis was performed using spss 20.0. continuous variables were expressed as means ± standard deviation (sd) using the student's t-test or as medians and interquartile range (iqr) using the mann-whitney u test. categorical variables were expressed as numbers (%) and compared by the χ 2 test or fisher's exact test. p< 0.05 was considered significant. of the 95 covid-19 patients, 44 were infected with influenza virus a, 2 with influenza virus b, 1 with adenovirus, 1 with parainfluenza; 47 were uninfected. a total of 93 patients were finally included, 46 (49.5%) of whom were infected with influenza virus a or b (classified as the flu group), while the rest (47; 50.5%) were uninfected (classified as the non-flu group). of these 93 patients, 44 were non-survivors and 49 were discharged. twenty-two (50.0%) non-survivors and 24 (49.0%) survivors were infected with the influenza virus. there was no significant difference in the proportion j o u r n a l p r e -p r o o f of patients co-infected with sars-cov-2 and the influenza virus between survivors and non-survivors. the median age of the 93 patients was 67.0 years (iqr 54.0-72.0) and females accounted for 45.2% of the total number of patients (table 1 ). the median time from illness onset to admission was 12.0 days (iqr 7.0-16.0) ( table 1) . chronic diseases were found in 53.8% of the patients, with hypertension being the most common, followed by diabetes and coronary disease ( table 1) . the most common symptoms on admission were fever, cough, and dyspnea, followed by chest distress/chest pain and fatigue ( table 1 ). the most common complication was ards, followed by acute cardiac injury, acute kidney injury, and liver dysfunction. among the non-survivors, the incidence of acute cardiac injury was significantly higher in the flu group (86.4%) than in the non-flu group (54.5%) (p< 0.05) ( table 2) . among the 93 patients, there was a significant difference in the proportion of patients with d-dimer levels >5μg/ml (ten times the normal d-dimer value) between the flu group (38.6%) and the non-flu group (11.4%) (p< 0.01), but no difference in white blood cell counts, neutrophil counts, lymphocyte counts, or levels of crp, alt, ast, ldh, creatinine, ctni, nt-probnp, tnf-α,and il-6 (p> 0.05) (data not shown). among the non-survivors, the white blood cell count, neutrophil count, tnf-α, d-dimer value, proportion of patients with d-dimer levels >5μg/ml, and proportion of patients with elevated creatinine levels were higher in the flu group than in the non-flu group (p< 0.05) ( table 3) most patients with severe covid-19 exhibit substantially elevated serum levels of pro-inflammatory cytokines, characterized as cytokine storm (cao 2020; mehta et al. 2020) . elevated cytokines also mediate extensive pulmonary pathology, leading to j o u r n a l p r e -p r o o f massive infiltration of neutrophils and macrophages (cao 2020) . neutrophil counts are increased in both the peripheral blood (wang et al. 2004 ) and lung (nicholls et al. 2003) among critically ill patients with severe acute respiratory syndrome. extensive pulmonary infiltration of neutrophils in patients with influenza induces lung tissue injury and worsens the disease (kulkarni et al. 2019 ). in our study, neutrophil and cytokine levels were generally elevated among the non-survivors, and the increment was more apparent among the non-survivors with influenza. co-infection with the influenza virus may further enhance neutrophil activation, thereby contributing not only to an excessive immune response against the virus, but also contributing to the development of a cytokine storm. studies have reported that elevated d-dimer levels are a risk factor for death in covid-19 patients (wu et al. 2020a; zhou et al. 2020) . we also found that the d-dimer levels of non-survivors were substantially higher than those of survivors. among the non-survivors, the d-dimer value was higher among patients with influenza than in those without influenza, which may have been due to local vascular injury, ischemia, and thrombosis caused by a viral infection-associated cytokine storm (davidson and warren-gash 2019) . our results further confirmed that co-infection with the influenza virus may induce an earlier and more severe cytokine storm in critically ill covid-19 patients, leading to serious complications such as shock, ards, fulminant myocarditis, acute kidney injure or multiple organ failure (cao 2020; ruan et al. 2020; wu et al. 2020a; zhou et al. 2020) . the current research had some limitations. first, the results of serological tests may be false-negative, especially within one week of infection or reinfection; or they may be false-positive due to long-term infections or carrier states. second, we were unable to determine the strains of influenza, and the infecting strain might affect the j o u r n a l p r e -p r o o f clinical characteristics. third, the included cases originated from wuhan, but differences in races and influenza strains among different countries may make covid-19 patients with influenza present different clinical characteristics. in addition, the number of included cases was small, and other factors such as gender, age, chronic disease, and time from illness onset to admission may have affected the results of this study. under the background of covid-19 global pandemic, the number of patients co-infected with sars-cov-2 and the influenza virus in some countries may increase as the flu season approaches. the clinical research of this co-infection, especially in the critically ill patients, will benefit global control efforts for 2020-2021. researches on different regions, races, age brackets, and influenza strains can reveal the epidemiological and clinical characteristics of co-infected patients more accurately, which requires larger sample sizes from multiple countries. furthermore, research from larger sample could contribute to unveiling whether this co-infection is the higher risk for severe disease or death associated with covid-19. to the best of our knowledge, this is the first study of co-infection with sars-cov-2 and the influenza virus among critically ill covid-19 patients. the results showed that a high proportion of covid-19 patients were co-infected with influenza in tongji hospital. co-infection with sars-cov-2 and the influenza virus may lead to a much earlier occurrence of the cytokine storm and organ damage in critically ill covid-19 patients. our results suggest that detection of the influenza virus should be considered in patients with covid-19, and that treatment strategies of anti-influenza virus and dampening inflammatory responses may be helpful for critically ill patients co-infected with sars-cov-2 and the influenza virus. the authors declare no conflict of interest. the submission of manuscript entitled "clinical characteristics of critically ill patients co-infected with sars-cov-2 and the influenza virus in wuhan, china" to "international journal of infectious diseases" for publication has been approved by all of the authors and by the institution where the work was carried out. all authors agree to abide by the journal's editorial policies and publishing ethics. there are not any competing interests on submission of this manuscript. j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f white blood cell count (×10 9 /l) 9.5(6.1, 13.6) 12.9(8.9, 15.4) 7.4(5.1, 11.0) 0.01 neutrophil count (×10 9 /l) 8.7(5.1, 12.6) 11.5(7.5, 13.6) 6.5(4.0, 10.0) 0.01 covid-19: immunopathology and its implications for therapy cardiovascular complications of acute respiratory infections: current research and future directions clinical characteristics of coronavirus disease 2019 in china epidemiology and arima model of positive-rate of influenza viruses among children in wuhan, china: a nine-year retrospective study excessive neutrophil levels in the lung underlie the age-associated increase in influenza mortality covid-19: consider cytokine storm syndromes and immunosuppression national health commission of people's republic of china. diagnosis and treatment for the novel coronavirus pneumonia (trial version 5) lung pathology of fatal severe acute respiratory syndrome novel coronavirus pneumonia emergency response epidemiology team clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan, china. intensive care med analysis of influenza surveillance in wuhan a cluster of patients with severe acute respiratory syndrome in a chest ward in southern taiwan risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease co-infection with sars-cov-2 and influenza a virus in patient with pneumonia, china. emerg infect dis clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study data are expressed as the median (iqr) or n/n (%), p-values are from the mann-whitney u test, χ² test or fisher's exact test. covid-19=coronavirus disease 2019 ast=aspartate aminotransferase; nt-probnp=amino-terminal pro-brain natriuretic peptide precursor we thank the staff members of tongji hospital for the management of patients.j o u r n a l p r e -p r o o f key: cord-304872-hnxmtbrf authors: lv, hao; zhang, wei; zhu, zhanyong; xiong, qiutang; xiang, rong; wang, yingying; shi, wendan; deng, zhifeng; xu, yu title: prevalence and recovery time of olfactory and gustatory dysfunctions of hospitalized patients with covid‑19 in wuhan, china date: 2020-09-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.039 sha: doc_id: 304872 cord_uid: hnxmtbrf objectives: to investigate olfactory and gustatory dysfunction in patients with coronavirus disease 2019 (covid-19) in wuhan using a telephone interview. methods: this retrospective telephone survey investigated 196 consecutive patients with covid-19 discharged 3 months previously from two hospital in wuhan, china. the characteristics of the patient's disease course and recovery time for olfactory and/or gustatory dysfunctions (od and/or gd) were collected by telephone interview. demographic data were collected from the patients’ medical records. results: a total of 196 patients with covid-19 completed the study. the most prevalent general symptoms consisted of fever, cough, and fatigue. 19.9% of patients reported od and/or gd. in 87.2% of these cases, od or gd appeared after the general symptoms. among the patients, 51.4% had a recovery time of more than 4 weeks for od and/or gd. patients with covid-19 and od and/or gd had significantly higher rates of cardiovascular disease than patients without od and/or gd (p = 0.002). conclusion: recovery from chemosensory dysfunction (od and/or gd) was slow, with over half of the patients taking more than 4 weeks to recover. cardiovascular disease might be related to the development of olfactory or taste disorders in patients with covid-19. the covid-19 pandemic is still spreading around the world at an exponential rate. to date, this infection, caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2), has infected millions of people worldwide and killed more than 450,000. early in the pandemic, chinese clinicians reported typical symptoms of the j o u r n a l p r e -p r o o f disease, such as fever, fatigue, cough, and dyspnea (guan et al., 2020) . however, the spread of covid-19 in the united states and europe has revealed some atypical symptoms of the disease, such as olfactory and gustatory dysfunctions (od and gd) speth et al., 2020) . few chinese studies have focused on olfactory and gustatory dysfunction in patients with . to the best of our knowledge, only one study has described these two symptoms. in their study of neurological symptoms of covid-19 infection, mao et al. (2020) found that 5.6% of patients had hypogeusia and 5.2% had hyposmia, which were the most common peripheral nervous system symptoms, which was much lower than that reported from europe and the united states. two hypotheses might explain the low prevalence of od and/ or gd reported in the chinese study: first, the number of chinese patients with covid-19 who exhibit olfactory or gustatory disorders is indeed lower. second, most early research in wuhan was based on the hospital medical records, and patients' sense of smell or taste might have been ignored by doctors during their medical history inquiry and records for the relative scarcity of medical resources during the early outbreak in wuhan. furthermore, all previous studies were limited to the acute phase with a short follow-up period, which might not reflect the recovery regularity of olfactory and/or gustatory impairment in patients with covid 19. in otolaryngology, olfactory and gustatory dysfunction following viral infection is not uncommon. unfortunately, in china, there is no professional group of ent physicians that has studied this condition. as of now, the mechanism by which patients with covid-19 develop od and/ or gd is unclear. it has been hypothesized that the development of od after sars-cov-2 j o u r n a l p r e -p r o o f infection may be related to direct damage to the olfactory bulb, to damage to olfactory receptor neurons in the olfactory epithelium, or both. and the ensuing change in taste may depend largely on olfactory impairment (ralli et al., 2020) . exploring the clinical features of these chemosensory disorders helps us to gain insight into the mechanisms behind them. therefore, we decided to collect detailed information about the od and/ or gd of patients with covid-19 using telephone interviews. the aim of this study was to investigate the occurrence and recovery time of olfactory and/or gustatory dysfunction in patients with covid-19 infection who were discharged from non-intensive care units 3 months earlier in china. we followed up 206 consecutive patients with covid-19 discharged from two hospital in wuhan, china (renmin hospital of wuhan university and wuchang mobile cabin hospital) between march 1 st and march 16 th , 2020. from the computerized database of these hospitals, we identified all adults hospitalized and diagnosed as having covid-19 by reverse transcriptase-polymerase chain reaction (rt-pcr) testing for sars-cov-2 from nasopharyngeal swabs. the exclusion criteria were as follows: patients under 18 years of age, patients with a history of cognitive disorders, and patients with od and/or gd known before the epidemic. demographic data including gender, age, and patient comorbidities and general symptoms were collected from the electronic medical record system of these hospitals. information about od and/or gd of each patient, including the duration of the symptoms and the recovering j o u r n a l p r e -p r o o f time were obtained by telephone interview. three trained otolaryngologists conducted telephone interviews with all participants using a standard questionnaire. all patients were then contacted by telephone up to three times to complete the study. we stopped the follow-up of the study on june, 20 th 2020. this study was approved by the ethics committee of renmin hospital of wuhan university (no. wdry2020-k148). spss software, version 24.0 (ibm corp, armonk, ny, usa) was used to perform all statistical analyses. data are presented as arithmetical mean values with the standard deviation (sd). the statistical significance of differences between data was evaluated using an independent sample t test. the chi-squared test was used to evaluate the constituent ratios in covid-19 with od and/or gd group and covid-19 without od and/or gd group. a level of significance of p < 0.05 was used. 206 patients were interviewed by telephone. 7 patients were excluded from the study because they could not be reached by phone three times. and 3 patients were unable to complete our questionnaire. so a total of 196 patients (95.1%) completed the survey. the mean age of the patients was 50.6 ± 13.8 years. there were 108 females and 88 males. the most common comorbidities of patients were hypertension, diabetes, and cardiovascular disease. table 1 shows the clinical and demographic characteristics of the patients. patients with covid-19 and od and/or gd had significantly higher rates of cardiovascular disease than patients without od and/or gd (p = 0.002). the two j o u r n a l p r e -p r o o f groups did not differ significantly in their general symptoms or other comorbidities (p > 0.05). of the 196 patients, 9.7% (39/196) reported smell and/or taste disorders. among them, 41.0% (16/39) and 23.1% (9/39) reported smell or taste disorders, respectively. in addition, 35.9% of patients (14/39) reported both smell and taste disorders ( figure 1 ). five of the 39 patients (12.8%) reported olfactory or gustatory dysfunction as their first symptom of covid-19 infection. the five patients stated that they exhibited typical symptoms, such as fever and cough, about 1 week after the onset of olfactory or gustatory dysfunction. thirty-four patients (87.2%) began to experience olfactory or gustatory disturbances following the appearance of general symptoms of covid-19 infection ( figure 2 ). among them, 85.3% of patients (29/34) reported chemosensory disorders (od and/or gd) within 8 days of the onset of general symptoms ( figure 2 ). the median time to develop od and/or gd after the onset of the typical symptoms was 3 days. by the end of follow-up, 10.3% of patients (4/39) indicated that their olfactory and/or gustatory function had not returned to normal, while 89.7% of patients (35/39) reported that the sense of smell and/or taste function was restored. figure 3 shows the recovery time pattern for the remaining 35 patients. only 8.6% of patients (3/35), od and/or gd recovered within 1 week of onset. it took more than 4 weeks for od and/or gd to return j o u r n a l p r e -p r o o f to normal in 51.4% of patients (18/35). two of the patients reported a recovery time of 2 months, which was the longest recovery time during our follow-up. figure 4 demonstrates the relationship between recovery time of patients with covid-19 with od and/or gd and overall patient-reported clinical improvement. recovery of the sense of smell and taste in most patients with covid-19 correlated temporally with overall clinical improvement of the disease. finally, we also compared the clinical characteristics of patients with a recovered sense of smell and/or taste and those who had not recovered their sense of smell and/or taste. there were no statistically significant differences in age, sex composition, or length of hospital stay between the two groups of patients (table 2 ). the spread of covid-19 is now accelerating worldwide, putting enormous pressure on every country's epidemic prevention efforts. studies have suggested od and/or gd as a screening criterion to identify patients with mild symptoms. however, the epidemiological characteristics and pathogenesis of these chemosensory disorders remain unclear. especially in china, there are few relevant studies. in this study, we performed subjective olfactory and gustatory evaluations in patients with covid-19 via telephone interviews. in addition, we analyzed the relationship between other symptoms of covid and chemosensory dysfunction using patients' electronic medical records and the telephone interviews. in the current study, 8.2% (16/196) and 4.6% (9/196) of patients reported olfactory and taste disorders, respectively. the low rates of od and/or gd in our study population j o u r n a l p r e -p r o o f are clearly contrary to those reported in european and american studies speth et al., 2020; chary et al., 2020) . in addition, a study from korea showed that 15% of patients with covid-19 had anosmia or ageusia, which was similar to our results ( lee et al., 2020) . however, a recent study showed that 38% of patients with covid-19 who self-reported as having an olfactory disorder showed normal in an objective olfactory test . therefore, the prevalence of covid-19related olfactory disorders might have been overestimated in studies based on subjective reports. in our study, most of the patients had od and/or gd following general symptoms such as fever, cough, and fatigue. the median time to onset of od and/or gd after general symptoms was 3 days. this meant that chemosensory disorders usually appeared early in the course of covid-19 infection. notably, in 5 of the 39 patients with chemosensory disorders, od and gd appeared before the other symptoms. in the context of the current pandemic, it is important for physicians to pay attention to patients who develop sudden od and gd, which are important for the early detection and isolation of patients with covid-19. similar to some previous studies chary et al., 2020) , women appear to be more susceptible to od or gd. in our cohort, 64.1% of patients with chemosensory disorders were female. however, meini et al. (2020) showed that women are less likely to develop chemosensory disorders compared with men. clearly, sex differences in patients with covid-19 with od or gd still require further study. one of the biggest concerns for all ent physicians and patients is the recovery time j o u r n a l p r e -p r o o f for od and/or gd. in the present study, over half of the patients with chemosensory disorders recovered over 4 weeks. however, our results contradicted those previous studies. klopfenstein et al. (2020) reported a mean duration of anosmia of 9 days, with a complete recovery occurring in almost all patients within 4 weeks. also reported that 72.6% of patients recovered their olfactory and gustatory functions completely within the first 8 days following resolution of the disease. in our study, all patients had complete recovery of overall disease symptoms within three weeks post-diagnosis. in contrast, more than half of the patients did not recover their olfactory or gustatory function during that time frame. although our results are preliminary, we concluded that the recovery time for chemosensory disorders in patients with covid-19 in the wuhan area is slow. we also sought to explore the differences in clinical characteristics between patients with a fully recovered sense of smell and/or taste and those with a partially recovered sense of smell and/or taste. however, there were no statistically significant differences in age, sex composition, or length of hospital stay between the two groups of patients. notably, all four patients who had not regained their sense of smell and/or taste by the end of follow-up were female. the pathophysiological mechanisms by which sars-cov-2 infection causes od or gd are unclear. a number of recent studies have explored the mechanisms that may lead to od or gd. zou et al. (2020) found that sars-cov-2 replicated particularly well in the nose, where a high viral load was detected shortly after the onset of symptoms. in addition, in the upper respiratory tract, nasal mucosal epithelial cells j o u r n a l p r e -p r o o f exhibited the highest expression of the sars-cov-2 receptor angiotensin i converting enzyme 2 (ace2), which increased the chance of viruses invading these cells and causing od (sungnak et al., 2020) . likewise, high expression of ace2 has been found in the tongue and oral mucosa, which might contribute to gd (xu et al., 2020) . nasal inflammation and obstruction might cause od and/or gd. however, mercante et al. (2020) found that most patients with a reduced sense of smell or taste did not report nasal congestion. during the telephone follow-up, we also asked patients about their nasal symptoms, including nasal obstruction, rhinorrhea (anterior and posterior), and sneezing. similarly, few patients indicated that they had any of these symptoms. apparently, there are other causes of od and/or gd following covid-19 infection. the invasion of sars-cov-2 through peripheral olfactory neurons, resulting in damage to the central nervous system, was considered a possible mechanism for the development of od (conde et al., 2020). brain magnetic resonance imaging of patients with covid-19 with anosmia noted abnormalities of the olfactory bulb and olfactory nerve aragão et al., 2020) . previous research on sars-cov also supported this hypothesis. netland et al. (2008) found that the virus can enter other areas of the brain through the olfactory bulb, creating rapid transmission across neurons. in fact, many of the clinical symptoms of covid-19 are suspected to be related to its nerve invasiveness. for example, a previous study showed that sars-cov-2 might cause respiratory failure in patients with covid-19 by attacking the respiratory center in the medulla oblongata . the slow relief of od and gd might be related to damage to the olfactory central nervous system. although the prevalence and prognosis of olfactory or gustatory disturbances in patients with covid-19 varies worldwide, the mechanisms underlying them remain unclear. some studies have shed some light on the mechanisms that underlie these differences. forster et al. (2020) identified three major variants, named type a, b, and c in a phylogenetic network analysis of 160 sars-cov-2 genomes. they found that type a followed by type c was predominant in europe and the united states, while type b was most common in east asia. phenotypic characteristics might differ between these variants, including those related to the prevalence of od and gd. in addition, the affinity of the virus for certain tissues and individuals might partially explain the clinical differences between patients in different parts of the world. the expression level of ace2, the receptor for sars-cov-2, in different tissues might be critical for the susceptibility, symptoms, and outcomes of covid-19 infection. a previous study on sars-cov showed that certain human ace2 variants show reduced binding to the sars-cov s protein (li et al., 2005) . similar to sars, the spike protein (s protein) of sars-cov-2 is responsible for entry into the host cell (wan et al., 2020) . by comparing 15 expression quantitative trait locus (eqtls) variants of the ace2 gene, the researchers found a large number of ace2 polymorphisms and differences in expression levels between the european and asian populations (cao et al., 2020) . we also compared the clinical characteristics of patients with covid-19 with a chemosensory disorder and those without a chemosensory disorder. the results indicated a significantly higher incidence of cardiovascular disease in patients with covid-19 with a chemosensory disorder than in patients with covid-19 without a j o u r n a l p r e -p r o o f chemosensory disorder. some studies have suggested that a decreased sense of smell is a predictor of cardiovascular disease development (schubert et al., 2015; siegel et al., 2019) . despite the small number of cases in our study, we speculated that cardiovascular disease might be related to the development of olfactory or taste disorders in patients with covid-19. there are some limitations to our study. the main limitation of our study is its retrospective nature, which might have led to recall bias. however, in patients with covid-19, olfactory or gustatory disturbances are relatively specific to other symptoms. in our telephone survey, the vast majority of patients were able to recall the onset and duration of the od and/or gd. the lack of full objective methods to assess olfaction may be considered as another weakness. considering the risk of crossinfection when performing objective tests, we decided to use a telephone interview in this study to learn about the patients' olfactory and gustatory functions. these shortcomings should be addressed in future research. the prevalence of olfactory and gustatory disorders associated with sars-cov-2 infection in china is much lower than that in the united states and europe. however, it is undeniable that od and/or gd is an early and even the first symptom of covid-19. as such, they help screen and identify patients with atypical symptoms. another characteristic of patients with covid-19 in china is the long recovery time from od and/or gd. cardiovascular disease might be related to the development of olfactory or taste disorders in patients with covid-19. however, because of the limited sample anosmia in covid-19 associated with injury to the olfactory bulbs evident on mri prevalence and recovery from olfactory and gustatory dysfunctions in covid-19 infection: a prospective multicenter study neurotropism of sars-cov 2: mechanisms and manifestations comparative genetic analysis of the novel coronavirus (2019-ncov/sars-cov-2) receptor ace2 in different populations clinical characteristics of coronavirus disease 2019 in china phylogenetic network analysis of sars-cov-2 genomes features of anosmia in covid19 olfactory and gustatory dysfunctions as a clinical presentation of mild-to-moderate forms of the coronavirus disease (covid-19): a multicenter european study prevalence and duration of acute loss of smell or taste in covid-19 patients objective olfactory evaluation of self-reported loss of smell in a case series of 86 covid-19 patients. head neck anosmia and olfactory tract neuropathy in a case of covid-19 the neuroinvasive potential of sars-cov2 may play a role in the respiratory failure of covid-19 patients receptor and viral determinants of sars-coronavirus adaptation to human ace2 neurologic manifestations of hospitalized patients with coronavirus disease olfactory and gustatory dysfunctions in 100 patients hospitalized for covid-19: sex differences and recovery time in real-life prevalence of taste and smell dysfunction in coronavirus disease severe acute respiratory syndrome coronavirus infection causes neuronal death in the absence of encephalitis in mice transgenic for human ace2 defining the burden of olfactory dysfunction in covid-19 patients olfactory dysfunction and sinonasal symptomatology in covid-19: prevalence, severity, timing, and associated characteristics. otolaryngol head neck surg sars-cov-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes inflammatory and vascular markers and olfactory impairment in older adults olfactory dysfunction persists after smoking cessation and signals increased cardiovascular risk receptor recognition by the novel coronavirus from wuhan: an analysis based on decade-long structural studies of sars coronavirus high expression of ace2 receptor of 2019-ncov on the epithelial cells of oral mucosa sars-cov-2 viral load in upper respiratoryspecimens of infected patients size, further research is needed to validate these results. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-311654-ixn65hxb authors: zumla, alimuddin; azhar, esam i.; shafi, shuja; memish, ziad a. title: covid-19 and the scaled-down 2020 hajj pilgrimage decisive, logical and prudent decision making by saudi authorities overcomes pre-hajj public health concerns date: 2020-08-08 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.014 sha: doc_id: 311654 cord_uid: ixn65hxb nan the abrupt appearance of sars-cov-2 as a novel lethal zoonotic pathogen causing disease in humans in late december, 2019 (who, 2020) , and its explosive global spread caught health authorities worldwide by surprise and exposed the ill-preparedness of global public health systems worldwide to deal with the appearance of a new pathogen. apart from generic prevention and control issues of public health and lockdown measures to limit epidemic spread, specific issues of mass gathering (mg) sporting and religious events came under specific spotlight (alzahrani et al, 2020; baloch et al, 2020; mccloskey et al, 2020; . mass gathering events present important health challenges related to the public health services and health of the host country population, the attendees and their home countries (memish et al, 2014; memish et al, 2019) . the 2009 hajj was held during the 2009 hin1 influenza pandemic and focused attention on developing mass gatherings medicine as a formal discipline, resulting in the formation of a coalition of global academic and public health faculty and virtual who mass gathering collaborating centres to guide development of, and update, optimal public health and medical prevention and treatment guidelines at mass gathering events (memish et al, 2014) . who with global mg partners, developed comprehensive key recommendations for covid-19, and since end of february, 2020, there was a stepwise increase in cancellation, temporary suspension or postponement of international and national religious, sporting, musical, and other mgs, as countries worldwide took public health and other measures (who, 2020b; mccloskey et al, 2020; petersen, mccloskey et al, 2020) . apart from focus on major sporting j o u r n a l p r e -p r o o f events, global focus has been on saudi arabia and the umrah and hajj pilgrimages. approximately 10 million people from 182 countries travel to saudi arabia annually for the hajj and umrah pilgrimages (memish et al, 2014; 2019) . the umrah pilgrimage can be performed anytime during the year saudi arabia with its extensive experience and commitment to pilgrim safety and wellbeing, was quick off the mark and on february 27th, 2020, restricted inbound flights and local and international pilgrims were prevented from travelling to makkah and madinah for the umrah pilgrimage. for the july 2020 hajj approximately 2.4 million pilgrims were expected in saudi arabia (saudi ministry of hajj and umrah, 2020) but they knew that the growing covid-19 pandemic may put their plans into disarray. the saudi ministry of health made regular announcements that the format of the hajj 2020 was being debated and evaluated based on covid-19 situation globally and domestically. several countries from where large numbers of muslim pilgrims originate (malaysia, indonesia, india and singapore) subsequently announced that they were barring their pilgrims from attending the 2020 hajj. these cancellations were anticipated to have major social and economic impacts on national economies, individual livelihoods and on public morale. the umrah and hajj pilgrimages together generate over $12 billion annually for businesses and the economy and limiting or cancelling the hajj would come at a huge cost. alzahrani et al (2020) in early june 2020, after careful consideration, the saudi government took decisive, logical, logistical and prudent decisions (saudi ministry of hajj and umrah, 2020) to overcome these pre-hajj nightmares of public health, political, economic and religious concerns. for the first time since the kingdom of saudi arabia was formed in 1932 the decision to bar pilgrims arriving in saudi arabia from foreign countries was made. the 2020 hajj was scaled down considerably, and participation for hajj rituals restricted to only 1,000 people with a negative covd-19 test, residing within the kingdom of which 'foreign' residents would comprise two thirds of all selected pilgrims from a pool of local workers, health care workers and security personnel especially those who had recovered from covid-19. those aged 65 years and over and those with co-morbid conditions would be barred. whilst all holy sites would remain open, adequate physical distancing and disinfection measures were put in place with j o u r n a l p r e -p r o o f oversight and assistance at regular intervals during the pilgrim's journey. wearing masks was mandatory and pilgrims would be subject to temperature checks and placed in quarantine if required. all pilgrims were given well thought out kits that include disinfectants, masks, a prayer rug, the ihram (a seamless white garment required to be worn by pilgrims), sterilised pebbles for the stoning ritual at jamaraat. throughout the pilgrims would have to keep a social distance of one and a half meters and were guided by well laid out markers and hajj coordinators. no pilgrims would be allowed to touch the kaaba or kiss the black stone at its corner -both of which are regular customs during the hajj. pilgrims would also have to be quarantined for 14 days after the pilgrimage. the hajj 2020 was a public health success and ended on monday 3 rd august, 2020. the decisive, logical and prudent decision making by saudi authorities which enabled the pre-hajj nightmare of public health, political, economic and religious concerns to be overcome. the successful completion of the 2020 hajj is a major tribute to the leadership and commitment of the saudi authorities, and it reflects their extensive experience of organising the annual hajj pilgrimage, and continued commitment to improvement public health issues related to mass gatherings events. the decisive actions, public health preparedness and strict implementation of public health prevention and intervention measures, pre-hajj, during hajj and post-hajj, serves as an exemplar for other mass gathering religious and sporting events. the 2020 hajj was not the first time the hajj has been scaled down. historically, the hajj has been scaled down several times before due to infectious diseases outbreaks. between 1830 and 1930, there were at least 27 cholera outbreaks among pilgrims in mecca (peters f,1994) . massive cholera outbreaks throughout the 19 th century resulted in the suspension of hajj in 1837 and 1846. the cholera outbreak in 1865 in saudi arabia led to establishment of quarantine ports to limit the spread of the disease during hajj. since saudi arabia's foundation in 1932 the hajj has never been cancelled and has not missed any year. the ongoing sars-cov-2 pandemic, yet once again, highlights the continuing threat of new emerging infectious diseases with epidemic potential, including the persistent threat of the middle east respiratory syndrome (mers) (perlman et al, 2020; memish et al, 2020b) to global health security. as of 2 nd august 2020, there have been 17,660,523 confirmed cases of covid-j o u r n a l p r e -p r o o f decisive leadership is a necessity in the covid-19 response forecasting the spread of the covid-19 pandemic in saudi arabia using arima prediction model under current public health interventions hajj in the time of covid-19 unique challenges to control the spread of covid-19 in the middle east saudi arabia's drastic measures to curb the covid-19 outbreak: temporary suspension of the umrah pilgrimage the continuing 2019-ncov epidemic threat of novel coronaviruses to global health -the latest 2019 novel coronavirus outbreak in wuhan, china a risk-based approach is best for decision making on holding mass gathering events hajj: infectious disease surveillance and control mass gatherings medicine: public health issues arising from mass gathering religious and sporting events pausing super spreader events for covid-19 mitigation: international hajj pilgrimage cancellation middle east respiratory syndrome confronting the persisting threat of the middle east respiratory syndrome to global health security the hajj: the muslim pilgrimage to mecca and the holy places covid-19 travel restrictions and the international health regulations -call for an open debate on easing of travel restrictions transmission of respiratory tract infections at mass gathering events saudi ministry of hajj and umrah the annual hajj pilgrimage-minimizing the risk of ill health in pilgrims from europe and opportunity for driving the best prevention and health promotion guidelines key planning recommendations for mass gatherings in the context of the current covid-19 outbreak infectious diseases epidemic threats and mass gatherings: refocusing global attention on the continuing spread of the middle east respiratory syndrome coronavirus (mers-cov) key: cord-291367-rtmsrh16 authors: zumla, alimuddin; rustomjee, roxana; ntoumi, francine; mwaba, peter; bates, matthew; maeurer, markus; hui, david s.; petersen, eskild title: middle east respiratory syndrome need for increased vigilance and watchful surveillance for mers-cov in sub-saharan africa date: 2015-07-02 journal: int j infect dis doi: 10.1016/j.ijid.2015.06.020 sha: doc_id: 291367 cord_uid: rtmsrh16 nan the past two decades have witnessed the emergence of several new and old respiratory tract infectious diseases, which threaten global health security due to their epidemic potential. 1,2 these include multi-drug resistant tb, severe acute respiratory syndrome (sars), avian and swine influenza and more recently the middle east respiratory syndrome (mers). mers is a new zoonotic disease of humans caused by a coronavirus (mers-cov) which was first isolated in september, 2012 from a patient who died from a severe respiratory disease in jeddah saudi arabia. 3 since then mers has attracted global media attention because it is associated with a high mortality (44%) in individuals who have co-morbidities such as diabetes, chronic renal, liver or lung illnesses or in those who are immunocompromised. 4, 5 the recent unprecedented outbreak of the mers 6, 7 in south korea which arose consequential to the importation of mers-cov by a south korean traveler to the middle east, alarmed global public health authorities and highlights the potential of mers-cov to spread across the globe and cause local outbreaks. the who director general convened the ninth meeting of the emergency committee (ec) under the international health regulations regarding mers-cov on 16 june 2015 to discuss the korean outbreak. 8 as of 23 rd june the total number of mers cases reported from the republic of south korea now stands at 175 (94 currently receiving treatment, 54 recovered, 27 deaths. 6, 8 of 175 cases, 80 patients and 33 hospital staff had contracted the virus nosocomially, 62 friends, colleagues and relatives had come in contact within healthcare facilities while visiting family members with mers. virological and serological studies from several middle eastern, west and east african countries indicate that bats and dromedary camels are likely reservoirs of mers-cov. [9] [10] [11] [12] however, human mers-cov infections appear to be endemic only to countries in the middle east where sporadic cases continue to occur in the community throughout the year. 13 13 the outbreak in seoul, republic of korea, has been linked to a single individual who had travelled to saudi arabia. the first mers case in thailand was reported last week and the patient had a history of travel from the sultanate of oman. 13 of note is the striking absence of any mers cases (primary or travel related) reported from sub-saharan african (ssa) countries. 14, 15 the reasons mers-cov predominantly affects humans in the middle east and is not endemic in africa where mers-covinfected camels and bats are present requires further study. a likely explanation may be that this may simply reflect the lack of clinical awareness of exposure risk, diagnosis and treatment of respiratory tract infections largely remains clinically based and empiric in most ssa countries coupled with absence of surveillance. 14 every year an estimated 10 million pilgrims from over 182 countries travel to the kingdom of saudi arabia to participate in hajj pilgrimage, the mini-pilgrimage umrah (which is performed at any time of the year), or for the month of ramadaan. 16 of these, an estimated 1 million pilgrims come from sub-saharan african countries. there were no cases of mers reported during the 2012, 2013 and 2014 hajj pilgrimages or the ramadaan period. [17] [18] [19] however, the risk of mers-cov spreading globally remains due to the continuous influx of pilgrims and the persistent low levels of endemic mers-cov transmission to humans in saudi arabia. there is also the possibility that mers-cov may mutate into a form more adaptable for human to human transmission over time. the potential risk of mers-cov infection to pilgrims who visit saudi arabia from different regions of the world was estimated by coker and colleagues 20 based on overall incidence of mers cases in saudi arabia since its first discovery in 2012. their estimates based on the most likely scenario using recent pilgrim numbers for sub-saharan africa are that there will be at most ten returning pilgrims each year with mers-cov infections. national surveillance systems should be on alert for the low but long-lasting risk of mers-cov infected pilgrims returning from the umrah throughout the year, and also for the large numbers of refugees at several conflict zones in the middle east (those migrating from syria to turkey and from the yemen border into saudi arabia and beyond). the recent mers outbreak in the republic of korea was associated with secondary, tertiary, quarternary and quinary cases of mers-cov transmission, though fortunately there has been no sustained community transmission. 6, 8 the republic of korea mers-cov outbreak has many similarities with that of previously reported mers-cov outbreaks which occurred at healthcare facilities in several cities in saudi arabia and from jordan 21-24 which were all associated with breaches and gaps in infection prevention and control protocols. these lapses in korean hospitals enabled mers-cov infected and uninfected patients, staff and visitors to mix freely in busy and crowded accident and emergency departments, within wards and multi-bed hospital rooms, with no isolation or quarantine of suspected cases. public health measures such as enhanced contact tracing and isolation and quarantine put in place by the korean government to control the outbreak eventually led to the decline in the numbers of mers cases and the outbreak is being brought under control. the importance of infection controls measures was also illustrated by the saudi arabian hospital mers outbreaks, where well-trained health care and workforce brought the hospital outbreaks under control quickly. 21, 22 the who ec meeting noted that 8 the who ec 8 referred to the outbreak as a 'wake-up' call and state that in a highly mobile world, all countries should always be prepared for the unanticipated possibility of outbreaks of mers-cov and other serious infectious diseases. the korean mers outbreak is the largest recorded from outside the middle east and the largest imported from a returning traveller to the middle east, raising several important issues for global surveillance and control. it illustrates that mers-cov, three years after its first discovery remains an important global public health risk with many unanswered questions. 25 further international spread should be anticipated and countries with weaker health systems and lack of laboratory facilities to accurately screen for mers-cov need to be vigilant. this will pose major challenges. 25 there are important lessons here for sub-saharan african and other developing countries from where mers-cov cases have not yet been detected. as the recent ebola virus disease epidemic illustrates, african countries may be very vulnerable to a korea-like mers-cov outbreak, which may arise from returning pilgrims or other travellers from saudi arabia 26 or from traders between saudi arabia and the horn of africa. mers-cov is transmitted through mers-cov-infected respiratory secretions for which contact and droplet precautions are recommended. [27] [28] [29] [30] the korean mers outbreak highlights that hospitals provide ideal conditions for amplifying mers-cov transmission arising from close contact between patients, healthcare and ancillary staff, relatives and other visitors, which enables spread of mers-cov. 6, 8 it is critical that every country should maintain a high level of vigilance and perform mers-cov surveillance according to widely available expert recommendations, 27-30 whether or not mers cases have been detected in their countries, it ensuring infection prevention and control protocols are in place at all health-care facilities. those who travel must be educated to follow basic hygiene measures 30 and those develop ill health during their trip to the middle east, or soon after their return should seek medical care and volunteer the history of travel to their healthcare provider. sub-saharan african governments must pay serious attention to strengthening infection control and public health surveillance systems. all healthcare workers and travellers from africa to the middle east should be aware of the threat to global health security posed by mers-cov. considering a diagnosis of mers at first presentation may be difficult due to non-specific symptoms at clinical presentation. however it is important that prevention and control measures are instituted at first consideration of mers as a diagnosis to prevent spread of mers-cov. hospitals and clinics providing care for patients infected with suspected or confirmed mers-cov infection should take appropriate measures to decrease the risk of mers-cov transmission from the infected patient to other patients, doctors, nurses, allied health-care workers, relatives and visitors. health-care workers should be educated and trained in infection prevention and control and should have continuing professional development on these issues. over the past decade, several surveillance systems have been introduced to monitor the emergence of new infectious pathogens. 31 as the ebola virus epidemic in west africa showed, surveillance systems in african countries for infectious diseases with epidemic potential require strengthening. more effective national, regional, and international surveillance systems are required to enable rapid identification of emerging respiratory epidemics, diseases with epidemic potential, their specific microbial cause, origin, mode of acquisition, and transmission dynamics. in light of the republic of korea mers outbreak increased vigilance and surveillance for mers-cov should be carried out by health services in african countries using current clinical and public health guidelines for mers-cov. 28 although resources may not allow for making an accurate diagnosis of mers, a high degree of awareness of the possibility of mers-cov infection in all returning pilgrims will allow early, isolation of patients and putting in place infection control measures, avoiding a repeat of the korea outbreak. sub-saharan african countries need to protect themselves against the possible outbreaks akin to the korean one. mers-cov should be included in list of pathogens by the african network of influenza surveillance and epidemiology (anise) 32 and mers-cov should be made part of the strengthening influenza sentinel surveillance in africa (sisa)' with national, regional and international reporting mechanisms 33 in liaison with other stakeholders involved in global infectious diseases surveillance. new, low cost, rapid, sensitive and specific diagnostic tests that can be used at all points of healthcare are require for all infectious diseases which threaten global health security. 34 the exact mode of transmission and pathogenesis of mers-cov and other novel respiratory tract viruses such as h7n9 influenza a virus require definition so that more effective prevention and management measures can be developed and introduced. 35 a united and coordinated global response is needed to tackle emerging respiratory tract infections and to fill major gaps 25 in the understanding of the epidemiology, transmission dynamics, pathogenesis prevention and control of these infectious diseases. declaration: all authors declare no conflicts of interest. emerging viral respiratory tract infections-environmental risk factors and transmission emerging infectious diseases and pandemic potential: status quo and reducing risk of global spread isolation of a novel coronavirus from a man with pneumonia in saudi arabia middle east respiratory syndrome severe acute respiratory syndrome vs. the middle east respiratory syndrome spread of mers to south korea and china who -ihr emergency committee concerning middle east respiratory syndrome coronavirus middle east respiratory syndrome coronavirus in bats, saudi arabia geographic distribution of mers coronavirus among dromedary camels mers coronavirus neutralizing antibodies in camels middle east respiratory syndrome coronavirus in dromedary camels:an outbreak investigation middle east respiratory syndrome coronavirus (mers-cov) -saudi arabia the hajj pilgrimage and surveillance for middle east respiratory syndrome coronavirus in pilgrims from african countries high prevalence of common respiratory viruses and no evidence of middle east respiratory syndrome coronavirus in hajj pilgrims returning to ghana hajj: infectious disease surveillance and control travel implications of emerging coronaviruses: sars and mers-cov etiology of severe community-acquired pneumonia during the 2013 hajj-part of the mers-cov surveillance program an update on middle east respiratory syndrome: 2 years later pilgrims and mers-cov: what's the risk? ksa mers-cov investigation team. hospital outbreak of middle east respiratory syndrome coronavirus an observational, laboratory-based study of outbreaks of middle east respiratory syndrome coronavirus in jeddah and riyadh, kingdom of saudi arabia mers-cov outbreak in jeddah-a link to health care facilities jordan mers-cov investigation team. hospital-associated outbreak of middle east respiratory syndrome coronavirus: a serologic, epidemiologic, and clinical description middle east respiratory syndromeadvancing the public health and research agenda on mers-lessons from the south korea outbreak coronaviruses: severe acute respiratory syndrome coronavirus and middle east respiratory syndrome coronavirus in travelers infection prevention and control of epidemic-and pandemicprone acute respiratory infections in health care -who guidelines. geneva, world health organization infection prevention and control during health care for probable or confirmed cases of middle east respiratory syndrome coronavirus (mers-cov) infection. update 4 th infection control advice -middle east respiratory syndrome coronavirus (mers-cov) middle east respiratory syndrome coronavirus (mers-cov): prevention in travelers surveillance for emerging respiratory viruses idsr as a platform for implementing ihr in african countries establishing a national influenza sentinel surveillance system in a limited resource setting, experience of sierra leone rapid point of care diagnostic tests for viral and bacterial respiratory tract infections-needs, advances, and future prospects emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options key: cord-273090-fdzkfo1u authors: he, susu; zhou, chao; lu, dongqing; yang, haihua; xu, hailing; wu, guixian; pan, weijia; zhu, rui; jia, haijian; tang, xinni; chen, xi; wu, xiaomai title: relationship between chest ct manifestations and immune response in covid-19 patients date: 2020-06-20 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.059 sha: doc_id: 273090 cord_uid: fdzkfo1u abstract objectives to study the and correlations of lymphocytes and cytokines between changes of lung lesion volumes in patients with covid-19, and to predict their correlation. methods 93 patients with covid-19 were divided into mild and severe groups. the data of lymphocyte subgroups and cytokines were collected, the imaging characteristics were measured and correlation analysis was performed to analyze the differences. results 60 mild and 33 severe patients were included, lymphocyte subsets decreased in both groups. the percentages of reduction of absolute lymphocytes value in mild and severe groups were 32% and 64% respectively. the lung ct lesion volume of all patients was 241.45 ± 282.92 cm3, among which the mild group was 151.29 ± 226.04 cm3 and the severe group was 405.38 ± 304.90 cm3, respectively. in critically ill patients, the decrease of absolute value of cd4 + t cells and increase of il-6 level are significantly correlated with the volume of lung lesions. conclusions the absolute values of cd3+, cd4+, and cd8 + t cells are lower in patients with covid-19, the levels of il-6 and il-10 are increased. the severity of lung lesions predicts poor clinical outcomes and may be a predictor of the transition from mild to severe. a group of unexplained pneumonia patients has been found in wuhan, china since december 2019. some of them have developed severe symptoms of acute respiratory infections, and some rapidly developed into acute respiratory distress syndrome and other serious complications. the chinese center for disease control and prevention (cdc) identified a novel β-corovirus in airway epithelial cells of patients and was named 2019-ncov by the who [1] . so far, infections have also been found in other cities in china and more than a dozen countries in the world, and there is increasing evidence that human-to-human transmission exists [2] [3] [4] . early studies have shown that increased pro-inflammatory cytokines in the serum of patients with sars are associated with lung inflammation and extensive lung injury [8] . there have been many reports that most of the 2019-ncov patients have chest ct manifestations of pneumonia, typically showing bilateral ground-glass shadows and patchy shadows, and a few can also appear as consolidation shadows and interstitial lesions, the laboratory showed that the lymphocytes count in most patients decreased [6] [7] [8] [9] , with gradually worsened the disease, the lymphocytes absolute count continued to decline [9] , and has been there are reports in the literature that the proinflammatory cytokines il-2, il-6, il-8, il-10, and tnf-α are elevated in some 2019-ncov patients [7] [8] . the purpose of this study is to investigate changes in lymphocytes counts and cytokines levels induced by 2019-ncov and their effects on lung lesions, to determine the severity of the disease, and to select markers that could prompt early clinical intervention. this study was a single-center retrospective study and recruited 93 2019-ncov patients who were admitted to taizhou public health medical center in zhejiang province from january 17 to february 12, 2020. taizhou public health center is the designated hospital for 2019-ncov patients in taizhou city, zhejiang province. according to the arrangements of the chinese government, when all patients diagnosed with 2019-ncov j o u r n a l p r e -p r o o f pneumonia in taizhou city according to the who interim guidelines [3] , all of them were obligated to be transferred to this center, followed by standard diagnosis and treatment. rt-realtime pcr confirmed that all patients were positive for the novel coronavirus nucleic acid. all patient data have been reported to the who. patients were divided into mild and severe (including severe and critical) groups according to the who ncp interim guidelines. this study was approved by the ethics committee of enze hospital, zhejiang enze medical group (center), and written informed consent was obtained from the patients before retrospective data collection. the patient's clinical symptoms, signs, laboratory test results, and treatment measures are all from electronic medical records. data related to other medical institutions are obtained directly by communicating with their attending physicians. the clinical results were followed up until february 27, 2020. the laboratory tests involved in this study include the absolute value of lymphocytes, cd3+t, cd4+t, cd8+t, b cell, nk cell, il-2, il-4, il-6, il-10, tnf-α , ifn-γ. we defined the patients' lung lesions including ground glass shadows, patch shadows, consolidation areas, interstitial lesions, and nodular shadows as our regions of interest (roi) (figure 1 ). in order to ensure the accuracy of the measurement, we have three physicians (all with more than 5 years of experience) to determine and measure the rio area. the number of measurements for each patient depends on the extent and scope of the lung lesions. the average value is the final measurement value. baseline characteristics, laboratory findings and radiology were compared using chisquare analysis. the variables of ct lesion area, lymphocytes and cytokines were compared using independent group t tests. the relationship of ct lesion area and peripheral blood lymphocytes were examined using the χ2 test. all statistical analyses were performed using sas version 7.0 software. for unadjusted comparisons, a 2-sided α of less than .05 was considered statistically significant. 93 patients with 2019-ncov infection were include in our study. patients were divided into mild and severe groups according to the who ncp interim guidelines. table 1 summarizes the characteristics of 2019-ncov patients, among which 60 were in the mild group (65%). 33 people were in the severe group (35%). the median age of the patients in the mild group was 44(44.5±12.5)years-old, and the median age of the patients in the severe group was 54(53.9±12.5)years. there was no statistical difference. this study shows that the most common symptoms of patients with this disease are fever (75%), followed by cough (65%), fatigue (24%), dyspnea (22%), myalgia (6%), sore throat (12%), and diarrhea (9%) are rare. twenty-four patients had at least one underlying disease, including 14 cases of hypertension, 7 case of diabetes and 2 cases of copd. the severe group (42%) was statistically different from the mild group (17%). among them, the number of patients with diabetes in the severe group was more than that in the mild group, p <0.05 table 2 shows the results of laboratory tests after admission. 40/ 93 patients (43%) had an absolute decrease in lymphocytes, among which 19(32%) patients were mild and 21(64%) patients were severe, there were statistical differences. t-cell subsets were tested in 73 patients, including 48 mild patients and 25 severe patients. among them, the absolute value of cd8 + t cell decreased in 34 (47%) patients, among which 17 patients were mild (35% of total mild patients), 17 cases of severe cases (68% of severe cases), p <0.05, there is a statistical difference. it was observed that some patients have decrease in cd3+ t cell (55%), cd4+ t cell (53%), b cell (21%), and nk cell (32%), but there was no statistical difference between mild or severe groups. all 93 patients were tested for il-2, il-4, il-6, il-10, tnf-α, and ifn-γ. there were 72 (77%) patients with elevated il-6, of which 42 were in mild patients (70% of the mild group) and 30 were in severe patients (91% of the severe group). there was a statistical difference between the two groups. there were 29 (31%) patients with elevated il-10, j o u r n a l p r e -p r o o f of which 13 were mild (22% of the mild group) and 16 were severe (48% of the severe group). there was a statistical difference between the two groups. il-2, il-4, tnf-α, and ifn-γ were normal in all patients. all patients underwent chest ct scans, and 71 (76%) patients had lesions involving 3 or more lung lobes, including all 33 critically ill patients. lung ct showed groundglass opacity or patchy shadowing in 88 (95%) patients, 50 (54%) patients with thickened lobular septum, 40 (43%) with consolidation, and 25 (27%) combined with nodular shadows, there were 4 (4%) mild patients with no abnormal chest ct. among them, severe patients had much more chances of consolidation than mild patients, which was statistically different ( table 3) . table 4 , the absolute values of lymphocytes, cd3+t cell, cd4+t cell, and cd8+t cell in the severe group had more significant decrease than those in the mild group, (p <0.05). the levels of il-6 and il-10 in the severe group were higher than those in the mild group, which was statistically significant (p <0.05). the lesion volume in lung ct in all patients were 241.45 ± 282.92 cm 3 . the volume of lung lesions in the light group was 151.29 ± 226.04 cm 3 , which was significantly smaller than that in the severe group (405.38 ± 304.90 cm 3 , p <0.001). in the mild group, the volume of the lung lesions was related to the absolute value of cd3+t cells and cd8+t cells, in severe patients, however, the volume of the lung lesions was correlated to the absolute value of cd4+t cells, p <0.05. although all patients' nk cells were within the normal range, the absolute value of the nk cells in the severe group was negatively correlated with the volume of lung lesions (p <0.05). (table 5) . no matter in the light group or the severe group, the size of the lung lesion volume was positively correlated with the increase of il-6, p <0.05 (table 6 ). similar to the study by wang et al. [9] , severe patients are generally older and have more comorbidities, which suggests that age and comorbidities are risk factors for adverse outcomes. the clinical characteristics of 2019-ncov infection are similar to those of previous beta coronaviruses such as sars-cov and mers-cov infection. in this study, the majority of patients presented with fever and dry cough, and a few were dyspnea, sore throat, nasal congestion, and diarrhea. the lung ct of most patients showed bilateral distribution of ground glass shadow and patchy shadow and lobular septum thickening, and patients can show consolidation shadows and nodular shadows, and a few patients have no obvious abnormalities in lung ct, which is similar to previous studies [6] [7] [8] [9] . the average age in this study is 49 years old. there is no significant difference between men and women, suggesting that 2019-ncov is generally susceptible to the population, which is different from previous reports [6] . similar to the study by wang et al. [9] , severe patients are generally older and have more comorbidities, which suggests that age and comorbidities are risk factors for adverse outcomes. lymphocyte subsets play an important role in human cellular immune regulation. studies have shown that the drastic reduction in the total number of lymphocytes indicates that coronavirus has consumed many immune cells and inhibited the body's cellular immune function. the damage of t lymphocytes may be an important factor leading to the deterioration of patients' conditions [13] . recently, the literature also pointed out that the decline of the absolute value of lymphocytes and the severity of chest ct manifestations predict poor clinical outcome [6] , which is consistent with the current literatures [14] . our study also showed that the absolute number of lymphocytes decreased in most patients, including cd3, cd4, cd8, b cells, and nk cells. in comparison with mild and severe patients, we found that cd4 + t, cd8 + t decreased, il -6, il-10 elevation is statistically significant, and it is found that patients with more profound lung lesions have more severely reduced lymphocytes counts, and the reduction is negatively correlated to the area of lung lesions. it can be seen that, like this study found that the serum levels of il-2, tnf-α, and ifn-γ were normal in patients, which is different from mers-cov infection and recent studies [12, 7, 16] , suggesting that 2019-ncov infection may not cause an inflammatory response. thelper-1 (th1) cells. similar to previous studies [7] , 2019-ncov infection led to an increase in il-6 and il10 associated with t-helper-2 (th2), which inhibits inflammation, and the levels of il-6 and il-10 increased significantly in severe patients compared with mild patients, which is different from sars-cov infection [10] . the results of this study indicate that th2-cell-associated il-6 and il-10 are involved in humoral immunity in patients with severe disease, which is higher than those in patients with mild disease, indicating that patients with severe 2019-ncov infection have stronger immune suppression. the above results suggest that we need to further study the response characteristics of th1 and th2 in 2019-ncov infection to clarify its pathogenesis our research shows that th2 related cytokines il-6, il-6 and il-10 are low or normal, which is similar to previous sars and other viral pneumonia findings [14] (6, 10 are not similar), but there are also studies showing that 2019-ncov infection causes increased secretion of t-helper-2 (th2) cytokines (such as il-4 and il-10) that suppress inflammation [7] , which is different from sars-cov infection [10] . the results of this study indicate that th2 cell-associated il-6 and il-10 in the severe group are higher than those in the mild group, indicating that the immunosuppressive effect of patients j o u r n a l p r e -p r o o f with severe infection is stronger. the above results suggest that we need to further study the response characteristics of th1 and th2 in 2019-ncov infection to clarify its pathogenesis. infection with sars-cov [8] , mers-cov [10] , and 2019-ncov can induce an increase in cytokines, and early studies have shown that increased inflammatory cytokines are related lung inflammation and acute lung damage [8] , il-6 may play a pro-inflammatory role in pulmonary inflammation [11] , and is closely related to mortality in ards patients [15] . our study observed that il-6 increased significantly in patients with severe inflammation in the lungs, and it's level changes accordingly as of inflammation increases and absorbs. it is suggested that the il-6 monoclonal antibody may reduce lung inflammation or may be used to treat 2019-ncov infection. it also suggests that for severe patients, early detection, early application of immunoglobulins to boost patients' anti-infective ability, early application of corticosteroids, reduction of alveolar damage and pulmonary exudation may improve patient prognosis. our study is not flawless. first, as a retrospective study, some clinical data is not complete. not all patients were tested for lymphocyte subsets and cytokines. a lot of cytokines are not included, for example il-1β, il-8, il-12, ip-10, csf, and transforming growth factor (tgf),.it is therefore difficult to clearly explain the changes of various cytokines caused by 2019-ncov infection and their impact on lung inflammation. in the future, more cytokine and chemokine studies are needed in prospective studies to clarify their potential as a prognostic indicator of the severity of 2019-ncov disease. we will continue to follow-up of cured and discharged patients, and regularly monitor the peripheral blood lymphocyte subsets, cytokines, chest ct, and lung function to reveal the impact of 2019-ncov infection on human long-term survival. we declare that we have no financial and personal relationships with other people a novel coronavirus emerging in china-key questions for impact assessment importation and human-to-human transmission of a novel coronavirus in vietnam clinical characteristics of 2019 novel coronavirus infection in china. medrxiv preprint clinical features of patients with 2019 novel coronavirus in wuhan epidemiological and clinical characteristics of 99 of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china plasma inflammatory cytokines and chemokines in severe acute respiratory syndrome diagnosis and treatment of adults with community-acquired pneumonia: an official clinical practice guideline of the mers-cov infection in humans is associated with a pro-inflammatory th1 and th17 cytokine profile differential role of interleukin-6 in lung inflammation induced by lipoteichoic acid and peptidoglycan from staphylococcus aureus induction of cytokines in mice with parainfluenza pneumonia t-cell immunity of sars-cov: implications for vaccine development against mers-cov characteristics of lymphocyte subsets and cytokines in peripheral blood of 123 hospitalized patients with 2019 novel coronavirus pneumonia (ncp) lymphocytes in the development of lung inflammation: a role for regulatory cd4+ t cells in indirect pulmonary lung injury this study was funded by the science and technology foundation of taizhou (number 1801ky18). we thank all patients involved in the study, and we acknowledge all health-care workers involved in the diagnosis and treatment of patients in taizhou, china. key: cord-282360-byqhzyzi authors: zhang, dingmei; lu, jiayuan; lu, jiahai title: enterovirus 71 vaccine: close but still far date: 2010-04-18 journal: int j infect dis doi: 10.1016/j.ijid.2009.12.002 sha: doc_id: 282360 cord_uid: byqhzyzi background: enterovirus 71 (ev71), a member of the enterovirus genus of the picornaviridae family, is one of the causative pathogens of hand-foot-and-mouth disease (hfmd) and the most common etiological agent isolated from hfmd patients complicated with neurological disorders. ev71 has become an increasingly important neurotropic enterovirus in the post-poliomyelitis eradication era. effective antiviral agents and vaccines against this virus are currently still under development. we reviewed publications on the development of ev71 vaccines in order to provide an overview of the field. methods: fifty-five articles on ev71 vaccine development, published from 1974 to 2009, were collected from sun yat-sen university library and reviewed. results: various types of vaccine have been developed for ev71. in results published to date, all vaccines for ev71 under development appear to elicit an immune response in rodents or in monkeys. according to the established regulatory standards, it may be relatively easy to acquire a license to use the inactivated virus in order to meet the immediate demands for ev71 control . with regard to the attenuated vaccine, it is critical to increase the genetic stability before clinical use, due to the risk of virulent revertants. the virus-like particle (vlp) vaccine, not only conserving the conformational epitopes, but also having no risk of virulent revertants, is another promising vaccine candidate for ev71, but needs further development. the vp1 capsid protein is the backbone antigen protein for developing subunit vaccine and epitope vaccine; these remain viable potential vaccine strategies worthy of further study and development. conclusions: the conservation of the three-dimensional structure is important for the ev71 inactivated vaccine and vlp vaccine to induce a strong immune response. to develop ev71 vaccines with a high protection efficacy, strategies such as the use of adjuvant, strong promoters, tissue-specific promoters, and addition of mucosal immune adjuvant should be considered. enterovirus 71 (ev71), a member of the enterovirus genus of the picornaviridae family, is the most frequently detected pathogen in hand-foot-and-mouth disease (hfmd) patients complicated with neurological dysfunction. 1 ev71 was first isolated in california in 1969, 2 and its association with hfmd was verified in 1974. 3, 4 it was later confirmed as the causative agent responsible for hfmd outbreaks in hungary, 5 australia, 6 hong kong, 7 taiwan, 8 japan, 9 and singapore. 10 moreover, in 2008 and 2009, a large outbreak occurred in mainland china. [11] [12] [13] children under 5 years of age have been found to be particularly susceptible to the severest form of ev71-associated neurological disease. 14 this is an important public health problem causing serious clinical illness and, potentially, death in young children. ev71 possesses a single-stranded rna genome of approximately 7500 nucleotides, consisting of a single open reading frame (orf) flanked by 5 0 -untranslated regions (5 0 utr) and 3 0 -untranslated regions (3 0 utr). the orf is expressed as a large polyprotein that can be cleaved into p1, p2, and p3 regions. the p1 region encodes four structural proteins vp1, vp2, vp3, and vp4. the p2 and p3 regions encode nonstructural proteins, such as proteases 2a, 2b, and 3cd, responsible for virus replication and virulence. protease 2a autocatalytically cleaves p1 at its n-terminus and liberates p1 from the nascent polyprotein, 15 while protease 3cd cleaves the p1 precursor into vp1, vp3 and vp0 (vp2 and vp4). these three structural proteins spontaneously assemble and form the crystalline virus-like particles. 16 though there has been a significant increase in ev71 epidemic activity throughout the asia-pacific region, effective antiviral therapies and vaccines have, to-date, not been available. the development of effective vaccines is a top priority in terms of control strategies. below is an overview of the field of ev71 vaccine preparation to date. background: enterovirus 71 (ev71), a member of the enterovirus genus of the picornaviridae family, is one of the causative pathogens of hand-foot-and-mouth disease (hfmd) and the most common etiological agent isolated from hfmd patients complicated with neurological disorders. ev71 has become an increasingly important neurotropic enterovirus in the post-poliomyelitis eradication era. effective antiviral agents and vaccines against this virus are currently still under development. we reviewed publications on the development of ev71 vaccines in order to provide an overview of the field. methods: fifty-five articles on ev71 vaccine development, published from 1974 to 2009, were collected from sun yat-sen university library and reviewed. results: various types of vaccine have been developed for ev71. in results published to date, all vaccines for ev71 under development appear to elicit an immune response in rodents or in monkeys. according to the established regulatory standards, it may be relatively easy to acquire a license to use the inactivated virus in order to meet the immediate demands for ev71 control . with regard to the attenuated vaccine, it is critical to increase the genetic stability before clinical use, due to the risk of virulent revertants. the virus-like particle (vlp) vaccine, not only conserving the conformational epitopes, but also having no risk of virulent revertants, is another promising vaccine candidate for ev71, but needs further development. the vp1 capsid protein is the backbone antigen protein for developing subunit vaccine and epitope vaccine; these remain viable potential vaccine strategies worthy of further study and development. conclusions: the conservation of the three-dimensional structure is important for the ev71 inactivated vaccine and vlp vaccine to induce a strong immune response. to develop ev71 vaccines with a high protection efficacy, strategies such as the use of adjuvant, strong promoters, tissue-specific promoters, and addition of mucosal immune adjuvant should be considered. ß 2010 international society for infectious diseases. published by elsevier ltd. all rights reserved. as conventional vaccines, inactivated virus vaccines, such as inactivated influenza vaccine 17 and inactivated hepatitis a vaccine, 18 have been successfully used in the human. seroepidemiologic studies have indicated that the preexisting neutralizing antibody to ev71 is protective against the severe outcomes of infection. 8, 19 yu et al. 20 and wu et al. 21 showed that passive transfer of serum from formalin-inactivated and heatinactivated virus vaccine immunized adult mice, could provide protection against ev71 challenge in neonatal mice; meanwhile, maternal immunization with inactivated ev71 vaccine was able to prolong the survival of suckling mice after ev71 lethal challenge. these results show the value of the inactivated virus vaccine for the effective control of ev71. however, the conservation of the threedimensional structure is important in order to induce a strong immune response. therefore, for the heat-inactivated virus, a much higher dose of viral antigen and adjuvant are required to achieve an acceptable level of immunogenicity and protection. obviously, an ideal vaccine strain is required for the large-scale preparation of the inactivated ev71 vaccine, as has been the case for the sabin oral polio vaccine (opv) strain. lin et al. 22 developed an ev71 strain, yn3-4a, exhibiting a rapid growth rate in vero cells with a larger plaque size and a lower lethal dose (ld) 50 in newborn mice. lin and coworkers showed that mouse antiserum raised against yn3-4a was able to neutralize a broad range of ev71 strains isolated from patients of a variety of geographic origins at different points in time. yn3-4a possesses desirable features, such as a high viral yield, the ability to propagate in serum-free medium, and strong immunogenicity, as well as broad-based antigenic coverage and passage stability, indicating its potential for development as an inactivated vaccine strain. a powerful cell system is also important in the development of an inactivated vaccine. as shown by wu and coworkers, 23 a serumfree vero cell culture with a 5 g/l cytodex 1 microcarrier concentration in a 2-l bioreactor has also been established, yielding a high titer of 5.8 â 10 7 tcid 50 /ml ev71 production. on the basis of the study of wu et al., 23 liu et al. 24 showed that the serum-free culture increased post-infection cell death and reduced the virus productivity, but elicited a higher neutralizing antibody titer in immunized mice as compared to the serum-containing cultures. therefore, the serum-free microcarrier culture is a valuable technique for developing inactivated ev71 vaccines on a large scale. an example of a successful attenuated strain vaccine is sabin opv. this was introduced in the early 1960 s due to its easier administration, lower cost, and higher intestinal muscosal immunity than the inactivated polio vaccine (ipv), and has since been approved for worldwide application for poliovirus eradication. 25, 26 because of the similarities between poliovirus and ev71, arita et al. 27, 28 have developed an ev71 attenuated strain, ev71 (s1-3 0 ), carrying mutations in the 5 0 utr, 3d polymerase (3d pol ) and 3 0 utr 5 0 non-translated based on the attenuation determinants of poliovirus. this ev71 (s1-3 0 ) strain is characterized by attenuated neurovirulence and limited spread of virus. in a subsequent study by arita et al., 29 three cynomolgus monkeys were inoculated with ev71 (s1-3 0 ), followed by a lethal challenge with the parental virulent strain ev71 (brcr-tr); they suffered mild neurological symptoms (tremor), but survived the lethal challenge without exacerbation of the symptoms. moreover, the sera from the immunized monkeys showed a broad spectrum of neutralizing activities against different genotypes of ev71. these findings indicate that ev71 (s1-3 0 ) acts as an effective antigen. however, it does cause mild neurological symptoms when inoculated via the intravenous route. additional studies are required to ensure that further attenuation produces effective attenuated vaccine strains. ev71 infection via the oral route did not efficiently cause neurological disorders in the inoculated monkeys. therefore the cynomolgus monkeys were inoculated by intravenous route instead of the oral route to evaluate the antigenicity of the attenuated ev71 vaccine. thus, to develop an oral ev71 attenuated vaccine, a valid animal model of ev71 infection by the oral route is urgently needed. meanwhile, it is well known that in a small number of opv recipients and their close contacts, especially those with primary humoral immunodeficiencies, the vaccine strain can mutate to a neurovirulent strain during opv replication and cause vaccineassociated paralytic poliomyelitis (vapp), which is an adverse side effect of opv. 30-32 a 1969 world health organization collaborative study found that the vapp rate was one in every 5.9 million doses administered for vaccine recipients and one in every 6.7 million doses administered for contacts. 33 therefore, the genetic stability of the attenuated opv is a major concern, and efforts should be made to further attenuate the neurotoxic effects and increase the genetic stability of the attenuated ev71 vaccine before clinical use. to overcome the potential problem of reversion to virulence of attenuated strain vaccine, subunit vaccines consisting of only one or a few 'subunit' proteins of the pathogen that can stimulate immune responses directed at the intact virus have been developed using recombinant dna technology. in common with other enteroviruses, the vp1, vp2, and vp3 of ev71 are responsible for the antigenic diversity of enteroviruses, but the vp1, the major capsid protein of ev71, is clustered with neutralization epitopes and has the potential to act as an antiviral subunit vaccine. 34 wu et al. 21 have described a recombinant vp1 protein expressed in escherichia coli bl21, showing that the vp1 protein with a complete adjuvant is able to elicit a neutralizing antibody response, enhance t helper cell proliferation, and induce high levels of interleukin (il)-10 and interferon (ifn)-g in mice, providing direct evidence that the vp1 protein contains neutralizing epitopes independent of other viral capsid proteins; this paves the way for the use of vp1 as a backbone antigen for developing subunit vaccines against ev71. transgenic edible plants and mammalian glands are possible alternatives to prokaryotic and eukaryotic cell culture systems, offering a palatable oral delivery system, which can elicit a good mucosal immune response as well as systemic humoral and cellular immune responses, making it particularly suitable for protecting against infectious agents intruding via the mucosal surface. 35,36 ev71 initiates disease following implantation in the gut mucosa, showing the potential of an oral vaccine for immunization against ev71 infection. chen and colleagues 37 have developed vp1-expressing transgenic tomato fruits. these were used as a mouse free-feeding oral vaccine. the vp1-specific fecal iga and serum igg were then observed in mice, and both humoral and cellular immunity against ev71 were established, showing the potential use of the transgenic tomato as an oral vaccine. meanwhile, other ev71 oral vp1 vaccine delivery systems, such as milk of transgenic mice described by chen et al. 38 and the salmonella-based method by chiu et al. 39 have been extensively explored. for oral vaccines, gastric acid and enzymatic digestion are major concerns, since they may interfere with vaccine absorption. the enterovirus genus can withstand human gastric acid and remain infectious below ph 3.0. however, vp1 is a capsid protein on the surface of the ev71 particle, and whether it can resist human gastric acid has not been fully addressed. meanwhile, digestive enzymes may also degrade the antigens. in the experiment of chen et al., mice gavaged with vp1 protein produced more vp1-specific antibodies than mice fed transgenic tomato containing more vp1 protein, in both sera and feces, indicating that chewing and digestion cause degradation of vp1 antigen. 37 also, the oral rotavirus vp4 protein vaccine has been shown to provide lower levels of antibodies and less protection than immunization by injection of the rotavirus vp4 protein, 40 indicating the possible interference of digestive enzymes. moreover, it has been difficult to determine the precise dose of antigens for immunization, since competition with food and microbial antigens interferes with the absorption rate of vaccine components. therefore, to improve oral vaccine delivery, many strategies have been developed, such as using tissue-specific promoters, the addition of mucosal immune adjuvant, using liposomes to protect the fusion peptides in the phospholipid bilayer vesicles from the gastric enzymes, and n-trimethyl chitosan nanoparticles. 41, 42 for the oral ev71 vp1 subunit vaccine, exploring strategies to protect antigens from enzyme degradation in the gut is necessary. dna vaccines are expressed intracellularly in the same manner as during natural viral infection and can stimulate either humoral immunity, cellular immunity, or both. 43 also, dna vaccines only deliver the target subunit antigen and thus cause fewer adverse effects, making them another valuable vaccine choice for most viral infections. tung and co-workers 44 developed an ev71 dna vaccine by inserting the vp1 gene into a eukaryotic expression vector and evaluated the immune response in mice. their study results showed that the anti-vp1 igg level increased in mice immunized with dna vaccine; in contrast, this level declined after boosting immunization. furthermore, although the anti-vp1 igg exhibited neutralizing activity against ev71, the neutralizing effect of the sera of mice immunized with the vp1 dna vaccine was much lower than that of ev71-infected human serum. another dna vaccine developed by wu et al., 21 elicited a high neutralization titer and stable titer level, which could be detected even at a late postimmunization time. however, because the dna vaccine contains fewer antigenic epitopes, it induces a weaker immune stimulation than the whole virus particles. therefore, strategies to increase the immune stimulation ability of dna vaccines have been developed including: incorporation of immunostimulatory sequences in the backbone of the plasmid, co-expression of stimulatory molecules, use of localization/secretory signals, and an appropriate delivery system, as well as adjuvants and optimization of transgene expression. 43, [45] [46] [47] all these techniques can help to prepare a better ev71 dna vaccine. an epitope peptide vaccine consisting of a well-defined immunogenic epitope stimulates an effective and specific protective immune response while avoiding potential undesirable effects. the host immune response developed upon any viral infection is primarily cd4+ t cell-dependent, including the induction of a cytotoxic cellular response and efficient antibody response. thus, identification of cd4+ t cell epitopes and b cell epitopes is of great importance in the design of effective epitope peptide vaccines. foo and colleagues [48] [49] [50] have published several studies aimed at identifying the t-cell and b-cell epitopes of ev71. in these studies, they identified three regions, 66-77, 145-159, and 247-261, spanning amino acids of the vp1 protein; they showed that these three regions could induce proliferation of cd4+ t cells, then producing abundant il-2 and ifn-g upon stimulation. additionally, among the three peptides, amino acids 145-159 induced the strongest proliferative response and highest cytokine production. furthermore, in order to identify the neutralizing linear epitopes, 95 overlapping synthetic peptides spanning the vp1 capsid protein of ev71 were used to immunize mice. 49 peptides containing amino acids 163-177 and 208-222 of vp1 protein were capable of eliciting neutralizing antibodies against ev71, and the neutralizing antibodies elicited by the synthetic peptide 208-222 were able to confer good in vivo passive protection against homologous and heterologous ev71 strains in suckling balb/c mice. 50 moreover, the monoclonal antibody generated by immunizing mice with amino acids 208-222 of vp1 showed strong neutralizing activity against ev71 in an in vitro neutralization assay. 51 therefore, the epitope peptide vaccine represents a promising candidate for ev71. the identification of more t-cell and b-cell epitopes of the vp1 protein, as well as a combination epitope peptide vaccine, should be considered in the search for a more effective epitope peptide vaccine. vlps are empty particles composed of all major structural proteins, mimicking the organizations and conformations of the native particles. to date, it has been shown that a wide range of vlps of clinically important viruses (e.g., hiv and severe acute respiratory syndrome coronavirus) induce effective neutralizing antibodies and cytotoxic t cell responses. 52, 53 the vlp vaccine, not only conserving the conformational epitopes, but also having no risk of virulent revertants, is also a promising vaccine strategy for ev71. hu et al. 16 and chung et al. 54 used a recombinant baculovirus expression system to express the 3cd and p1 proteins of ev71; the 3cd protein cleaves p1 precursor into vp1, vp3, and vp0, which spontaneously assemble to form vlps, inducing both th1 and th2 immune responses. more importantly, the vlp immunization of mother mice conferred protection to neonatal mice against the lethal viral challenge, indicating ev71 vlp to be a promising vaccine. chung et al. 55 also found that compared with the intact vlps, the denatured vlps elicited significantly lower levels of neutralizing antibodies and conferred lower degrees of protection against virus challenge, which highlights the importance of preserving the conformation-dependent epitopes in preventing ev71 infection. at present, the vlps are mostly developed using insect cells and the strict culture conditions limit the required large scale of vaccine production. thus, transgenic plants or yeast that can produce vlps to be delivered by either oral administration or injection, might be promising expression systems. ev71 is one of the causative pathogens of hfmd, often complicated with neurological disorders. due to the similarities between poliovirus and ev71 in many virological and clinical aspects, the success of the oral polio vaccine and inactivated-virus preparation in controlling poliomyelitis and eradicating the poliovirus, highlight the potential for controlling ev71 by vaccination. poliovirus vaccine technology, both live attenuated and inactivated virus vaccines, can be adapted to control ev71 infection. in recent years, various types of vaccine against ev71 have been developed, but these have as yet remained at the preclinical stage. outbreaks of ev71 have been reported around the world since 1969. in economically developed nations, it typically causes a mild illness, and most patients usually recover quickly. however, since the late 1990 s, there has been a significant increase in ev71 epidemics, and it has emerged as a serious threat to public health throughout the asia-pacific region. developed countries with the resources for vaccine research and development do not view ev71 as a priority, and the vaccine industry in developed countries has little incentive to develop a vaccine to ev71. at present, there are only a few vaccine industries in the asia-pacific region undertaking ev71 vaccine preparation. therefore, to effectively control ev71, more effort and cooperation worldwide is needed. because ev71 mainly threatens the children in developing countries, an ideal ev71 vaccine would have to be inexpensive, safe, convenient to administer, and acceptable to parents. for the inactivated virus vaccine, the established regulatory standards may allow a license to be obtained to meet the immediate demands for ev71 control. due to the need to conserve the threedimensional structure, the formalin-inactivated virus vaccine is a potential candidate vaccine for ev71. an oral ev71 attenuated vaccine has the potential to control ev71 in the same way as opv controlling poliovirus, though further attenuation procedures are needed. at present, there are five genotypes of ev71. crossprotection to the different genotypes for all the ev71 vaccines under current development is unclear. hence, the preparation of a vaccine strain providing wide cross-protection is another important issue for ev71 vaccine development. there are no conflicts of interest with regard to employment, consultancy, stock ownership, honoraria, paid expert testimony, patent applications/registrations, or grants. we declare that we have no funding source. outbreaks of hand, foot, and mouth disease by enterovirus 71. high incidence of complication disorders of central nervous system an apparently new enterovirus isolated from patients with disease of the central nervous system new enterovirus type associated with epidemic of aseptic meningitis and-or hand, foot, and mouth disease a large-scale epidemic of hand, foot and mouth disease associated with enterovirus 71 infection in japan in 1978 virological diagnosis of enterovirus type 71 infections: experiences gained during an epidemic of 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constructs against enterovirus 71 elicit immune response in mice intradermal immunization with novel plasmid dnacoated nanoparticles via a needle-free injection device chemical adjuvants for plasmid dna vaccines dna vaccines: improving expression of antigens identification of human cd4 t-cell epitopes on the vp1 capsid protein of enterovirus 71 identification of neutralizing linear epitopes from the vp1 capsid protein of enterovirus 71 using synthetic peptides passive protection against lethal enterovirus 71 infection in newborn mice by neutralizing antibodies elicited by a synthetic peptide generation of neutralizing monoclonal antibodies against enterovirus 71 using synthetic peptides chimeric gag-v3 virus-like particles of human immunodeficiency virus induce virus-neutralizing antibodies assembly of human severe acute respiratory syndrome coronavirus-like particles expression, purification and characterization of enterovirus-71 virus-like particles immunization with virus-like particles of enterovirus 71 elicits potent immune responses and protects mice against lethal challenge we would like to express our thanks to associate prof. xia guo (the hong kong polytechnic university), dr. zhiyong guo (sun yatsen university) and dr. e. mengue mengue (sun yat-sen university) for their help in manuscript modification. key: cord-311479-8pjoz64q authors: he, daihai; zhao, shi; lin, qianying; zhuang, zian; cao, peihua; wang, maggie h; yang, lin title: the relative transmissibility of asymptomatic cases among close contacts date: 2020-04-18 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.034 sha: doc_id: 311479 cord_uid: 8pjoz64q abstract asymptomatic transmission of the coronavirus disease 2019 is an important topic. a recent study in china showed that transmissibility of the asymptomatic cases is comparable to that of symptomatic cases. here we showed that the conclusion may depend on how we interpret the data. to the best of our knowledge, this is the first time the relative transmissibility of asymptomatic covid-19 cases is quantified. asymptomatic transmission of the coronavirus disease 2019 is an important topic. a recent 24 study in china showed that transmissibility of the asymptomatic cases is comparable to that 25 of symptomatic cases. here we showed that the conclusion may depend on how we interpret 26 the data. to the best of our knowledge, this is the first time the relative transmissibility of 27 asymptomatic covid-19 cases is quantified. 28 29 keywords: covid-19; asymptomatic cases; relative transmissibility 30 31 32 33 main text 35 nishiura et al (nishiura et al, 2020 ) estimated the asymptomatic ratio of covid-19 was 41.6% 36 (5 out of 12 confirmed cases) among 565 japanese individuals evacuated from wuhan, china. 37 mao et al (mao et al, 2020) reported that 2 out of 78 confirmed cases are asymptomatic. one 38 of the two cases showed rt-pct positivity 15 th days after first diagnosis. mizumoto et al 39 estimated that the 17.9% of cases on the diamond princess cruise ship were asymptomatic 40 case during the outbreak in february 2020 (mizumoto et al, 2020) . however, the 41 transmissibility of asymptomatic case is unclear, and the positive rt-pct results only imply 42 the potential infectivity. it is important to study the pattern of viral shedding and live virus 43 isolation. wölfel et al studied 9 hospitalized cases and found that live virus was isolated from 44 throat and lung-derived samples between 3 and 8 days after symptom onset (wölfel et al, 45 2020) . when the rna concentration is above 10 6 copies per ml (or equivalent ct-value lower 46 than 24), but not from stool samples, despite of high virus rna concentration. above the 47 threshold, high rna concentration yields high probability of live virus isolation. this 'dose-48 response' association highlights a patient's rt-pcr level should be higher than a threshold 49 to be effectively infectious. however, the mean infectious period (γ −1 ) of a symptomatic case may be longer than that of 102 an asymptomatic case hypothetically. therefore, the combined effects of ρ and γ −1 probably 103 lead to a higher reproduction number in the symptomatic group. 104 105 additionally, chen et al (chen et al, 2020) showed that asymptomatic cases are more likely 106 to produce asymptomatic cases relatively speaking, since the 6 secondary cases from 107 asymptomatic primary cases consist 3 asymptomatic cases (50%). whereas, 19 out of 126 108 (15%) are asymptomatic from symptomatic primary cases. the odds ratio (or) is estimated 109 in summary, we conclude that the relatively transmissibility of asymptomatic case could be 127 significantly smaller than that of the symptomatic cases. the main contribution of (chen et al, 128 2020) is that they raise the alarm of the existence of the transmissibility of the asymptomatic 129 cases. we remark that how efficient of the transmissibility of asymptomatic cases comparing 130 to symptomatic cases warrants more study. 131 132 133 here we showed that the conclusion may depend on how we interpret the data. 287 288 we also reported the asymptomatic case ratio in hong kong over time due to a large number 289 of young imported case. 290 291 to the best of our knowledge, this is the first time the relative transmissibility of 292 asymptomatic covid-19 cases is quantified. 293 294 295 estimation of the asymptomatic ratio of novel coronavirus infections (covid-158 19) estimating the asymptomatic 161 proportion of coronavirus disease 2019 (covid-19) cases on board the diamond princess 162 cruise ship the enlightenment from two 165 cases of asymptomatic infection with sars-cov-2: is it safe after 14 days of 166 isolation? sars-cov-2 169 viral load in upper respiratory specimens of infected patients virological assessment of hospitalized patients 174 with covid-2019 coronavirus disease 2019 in china. the new england journal of medicine serial interval of covid-19 180 among publicly reported confirmed cases. emerging infectious diseases covert coronavirus infections could be seeding new outbreaks the 185 epidemiological characteristics of infection in close contacts of covid-19 in ningbo city modelling the coronavirus disease (covid-19) outbreak on 190 the diamond princess ship using the public surveillance data from dh was supported by an alibaba (china)-hong kong polytechnic university collaborative 237 research project. other authors declared no competing interests key: cord-279892-37vyazby authors: sun, guanghao; nakayama, yosuke; dagdanpurev, sumiyakhand; abe, shigeto; nishimura, hidekazu; kirimoto, tetsuo; matsui, takemi title: remote sensing of multiple vital signs using a cmos camera-equipped infrared thermography system and its clinical application in rapidly screening patients with suspected infectious diseases date: 2017-01-16 journal: int j infect dis doi: 10.1016/j.ijid.2017.01.007 sha: doc_id: 279892 cord_uid: 37vyazby background: infrared thermography (irt) is used to screen febrile passengers at international airports, but it suffers from low sensitivity. this study explored the application of a combined visible and thermal image processing approach that uses a cmos camera equipped with irt to remotely sense multiple vital signs and screen patients with suspected infectious diseases. methods: an irt system that produced visible and thermal images was used for image acquisition. the subjects’ respiration rates were measured by monitoring temperature changes around the nasal areas on thermal images; facial skin temperatures were measured simultaneously. facial blood circulation causes tiny color changes in visible facial images that enable the determination of the heart rate. a logistic regression discriminant function predicted the likelihood of infection within 10 s, based on the measured vital signs. sixteen patients with an influenza-like illness and 22 control subjects participated in a clinical test at a clinic in fukushima, japan. results: the vital-sign-based irt screening system had a sensitivity of 87.5% and a negative predictive value of 91.7%; these values are higher than those of conventional fever-based screening approaches. conclusions: multiple vital-sign-based screening efficiently detected patients with suspected infectious diseases. it offers a promising alternative to conventional fever-based screening. since the outbreak of severe acute respiratory syndrome (sars) in 2003, infrared thermography (irt) systems have been used as border-control devices at most major international airports to screen passengers for fever. irt remains the gold standard for border control, because it can rapidly mass-screen infected individuals without contact. [1] [2] [3] [4] however, irt measurements are influenced by several factors, including the environmental temperature and humidity, alcohol consumption, and the consumption of antipyretic medications. 5 body temperature, in particular, can be modified rapidly by the consumption of antipyretic drugs, which directly affects the sensitivity of irt. hence, fever-based screening using irt suffers from low sensitivity. this paper describes a combined visible and thermal image processing approach that uses a complementary metal oxide semiconductor (cmos) camera-equipped irt system that may address this issue. these systems have already been installed at most major international airports, and they can remotely sense several vital signs, including body temperature and heart and respiration rates, thereby facilitating the rapid and accurate screening of people who are suspected of carrying infectious diseases. the concept underlying vital-sign-based screening is based on the association between infections and inflammation. inflammation causes elevations in body temperature and in heart and respiration rates; therefore, integrating vital sign monitoring increases screening accuracy. this concept was used in previous studies by the present author group to develop a novel infection screening radar system to mass-screen individuals. this system utilizes a multisensor fusion technique to remotely measure heart and respiration rates using a microwave radar, and the facial skin temperature is measured using irt. the results from case-control studies that investigated seasonal influenza screening showed a detection accuracy that ranged from 81.5% to 98.0% using the heart and respiration rates and the facial skin temperature, which is higher than the detection accuracies of the conventional feverbased screening methods. [6] [7] [8] [9] however, the radar system used to screen for infections incorporates expensive embedded multisensor modules, namely a microwave radar, a reflective photoplethysmography sensor, and irt, and it requires large-scale systems. consequently, the system is not used widely. hence, to promote the widespread use of vitalsign-based screening, focus has been placed on systems with minimum hardware requirements to achieve a system that is more suitable for real-world settings. the most reliable solution is to enhance the functionality of the conventional irt systems that are already installed at international airports. by incorporating the latest advances in image processing techniques, these irt systems can acquire thermal and visible images together by integrating visible and thermal cameras. in this study, high image and temperature resolution irt that combines visible and thermal images was used to acquire multiple vital sign measurements from facial images using remote sensing. the benefit of this approach is that it only requires a cmos camera that is equipped with irt rather than a large-scale system. technical details of the system and the evaluation of its laboratorybased performance have been described in a previous publication. 10 respiration rates are measured by monitoring the temperature changes around the nasal area that are associated with inspiration and expiration; the facial skin temperature can be determined easily from the thermal images simultaneously. the circulation of blood in the face causes tiny color changes that provide a visible facial image that can be used to determine the heart rate. 11 a multiple logistic regression function is incorporated into the system to predict the possibility of infection; hence, irt can automatically detect infected individuals based on their vital signs, which are measured in real time. this system was tested on patients with an influenza-like illness in a clinical setting to evaluate the performance of this vital-sign-based screening approach using irt alone. visible and thermal image processing method to remotely sense multiple vital signs this method has been described in detail from an imageprocessing perspective in a previous publication. 10 a cmos camera-equipped irt system (tvs-500; nec/avio infrared technologies co. ltd, tokyo, japan) was used; this is the same system that is used in the quarantine station at narita international airport in japan. 5 the irt system integrates a cmos camera with thermography to capture visible and thermal images, respectively ( figure 1 ). the visible and thermal images were recorded at a speed of 30 frames per second and at a resolution of 640 â 480 pixels. the circulation of blood in the face causes tiny color changes on facial images that are undetectable with the human eye. the cmos camera uses this information to determine the heart rate. to measure the respiration rate from the thermal images, the temperature changes that occur around the nasal area during the inspiration of cold air from the environment and the expiration of warm air from the lungs was monitored, and the respiratory waveform was extracted from the differences in each of the thermal images. this enabled the respiration rate to be determined from the breath-to-breath intervals. the facial skin temperature was measured simultaneously using the thermal images. the image acquisition and processing programs were written in labview software (national instruments, texas, usa). subjects were seated in front of the irt system at a distance of approximately 0.5 m. the irt system displays the 'infection' or 'healthy' result within 10 s using the logistic regression discriminant function, which bases the output on the heart rate, respiration rate, and facial skin temperature. this was a cross-sectional investigation that was undertaken at the takasaka clinic in fukushima in japan. the study involved 16 outpatients (11 male and five female) who visited the takasaka clinic with an influenza-like illness that included fever, headache, and sore throat, between january 22, 2015, and february 25, 2015. the ambient temperature (around 23.0 c) was also monitored to ensure reproducible environmental conditions. the average axillary temperature of the patient group was 37.2 c (range <36.2-< 39.0 c), and their average age was 36 years. the 22 healthy control subjects (10 male and 12 female) were students and admissions staff from tokyo metropolitan university, japan, none of whom had a fever, headache, or sore throat. the average axillary temperature of the control group was 36.3 c (range <35.4-< 37.0 c), and their average age was 35 years. in this study, abnormal vital signs were defined according to the diagnostic criteria for systemic inflammatory response syndrome (sirs), i.e., (1) body temperature >38 c or <36 c, (2) heart rate >90 bpm, and (3) respiration rate >20 breaths/min. this study was approved by the faculty of system design committee on human research at tokyo metropolitan university. logistic regression discriminant analysis to predict the possibility of infection based on the vital signs measured to distinguish between patients with infectious influenza and healthy control subjects, logistic regression discriminant analysis was used to establish a classification model based on the three derived vital signs. multivariable logistic regression analysis is a well-established statistical method that is used to analyze dichotomous outcomes in clinical practice; it is flexible and robust, and enables meaningful data interpretations. 12 moreover, logistic regression analysis is much easier to implement in a real-time classification system, and saves computation time, compared with other classification methods such as neural network computation. the logistic regression discriminant function was defined as: where p i is the probability of the outcome of infection, b 0 is a constant, b 1 , b 2 , and b 3 are the regression coefficients corresponding to the respiration rate, heart rate, and facial skin temperature, respectively, and x 1 , x 2 , and x 3 are the three vital sign variables of the respiration rate, heart rate, and facial skin temperature, respectively. the results from the logistic regression classification model were used to calculate the sensitivity, specificity, negative predictive value (npv), and positive predictive value (ppv) using a 2 â 2 contingency table. 13 to avoid overfitting, a leave-one-out cross-validation was performed. the mean and standard deviation (sd) values of the three vital signs were calculated. the differences between the influenza patients and the healthy control subjects with respect to the three vital signs were evaluated using the mann-whitney u-test. a p-value of <0.05 was considered to indicate statistical significance. the classification model was established using the data that described the three vital signs from the 16 influenza virus-infected patients and the 22 healthy control subjects using multivariable logistic regression. the statistically significant model is shown below: where x 1 is the respiration rate, x 2 is the heart rate, and x 3 is the facial skin temperature. the derived logistic function, z(x 1 ,x 2 ,x 3 ), was statistically significant (p < 0.05). the z(x 1 ,x 2 ,x 3 ) value could be used to differentiate patients with influenza (z ! 0) from healthy subjects (z < 0). figure 2 illustrates the discrimination results that were obtained by plotting the z(x 1 ,x 2 ,x 3 ) values against the axillary temperatures of the two groups. of the patients with influenza, 14 (red dots) are enclosed within the red ellipse and they had positive z-values, and two patients had negative z-values ( figure 2 ). the 22 healthy control subjects (blue dots) enclosed within the blue ellipse had negative z-values and none of the healthy subjects had a positive z-value ( figure 2) . therefore, the sensitivity, specificity, npv, and ppv were 87.5%, 100%, 91.7%, and 100%, respectively. the fever-based screening, for which the cut-off value for the axillary temperature was set at 37.0 c, did not detect five influenza patients (false-negative). the sensitivity of the fever-based screening was 68.7%. table 1 presents a more detailed comparison of the patients with influenza and the healthy control subjects. the influenza patients who had higher z(x 1 ,x 2 ,x 3 ) values had more severe symptoms, namely higher body temperatures and more elevated heart and respiration rates. the classification model determined that some patients had influenza, even if they did not have a fever. the z(x 1 ,x 2 ,x 3 ) values could be used to evaluate the severity of infections, and they could, therefore, support the clinical risk stratification of patients. the two influenza patients who were misclassified had negative z-values because their vital signs were normal. the mean (sd) facial skin temperature of the influenza patients (36.4 (0.7) c) was 1.1 c higher than that of the healthy control subjects (35.3 (0.6) c). the mean (sd) heart rate of the influenza patients (86.7 (12.1) bpm) was 21.3 bpm faster than that of the healthy control subjects (65.5 (6.8) bpm). the respiration rate did not differ significantly between the influenza patients (19.8 (5) breaths/min) and the healthy control subjects (19.5 (5) breaths/ min) (figure 3 ). an integrated visible and thermal image processing approach is proposed for the remote monitoring of multiple vital signs using irt, thereby enabling the rapid screening of infection in places of mass gathering. the results of this study demonstrate that the effectiveness of irt for the screening of infection can be greatly enhanced by measuring body temperature, as well as heart and respiration rates, using irt without any additional sensors. the high level of accuracy of the automated irt system has a number of clinical implications that could enable the system to be used to provide primary screening of people who may be carrying infections within emergency outpatient units or quarantine stations. moreover, this system saves time, because considerable amounts of time are required to investigate false-positive subjects when systems have low sensitivity levels and npvs. this technology also opens up new opportunities for controlling the spread of infections. for example, the present study was conducted at the takasaka clinic in fukushima prefecture, which is one of the three prefectures that were most affected by the 2011 earthquake and tsunami in japan. 14 the risk of contracting infectious diseases, particularly influenza, increased after the earthquake and tsunami in fukushima, and healthcare table 1 comparisons between the patients with influenza and the healthy control subjects. zðx 1 ; x 2 ; x 3 þ value (z ! 0) x 2 respiration rate (bpm) x 2 heart rate (bpm) figure 3 . mean (standard deviation) values were calculated for the three vital signs. the differences between the influenza patients and the healthy control subjects with respect to heart rate, respiration rate, and facial skin temperature were assessed. ns, not significant. professionals and medical facilities were severely affected by the disaster. 15, 16 in such settings, an automated irt system could distinguish between individuals who are and are not carrying infections, thereby alleviating the workload of healthcare professionals. therefore, the proposed integrated visible and thermal image processing approach may be a promising pre-examination technique in disaster settings. limitations of the present study mostly pertain to data samples (16 patients and 22 healthy control subjects), which can be considered sufficient for evaluation by the cmos camera-equipped irt system for vital-sign measurement. however, the data samples are small for training in a logistic regression classification model. to refine the performance of the logistic regression classification model implemented in the irt system, field testing with larger and completely random subject populations will be conducted in realworld settings. moreover, to guarantee the accuracy of heart and respiration rate measurement by the irt system, the authors are now working on the development of an automatic real-time human face tracking algorithm using visible and thermal images. detecting and tracking human faces can significantly reduce motion artifacts, thereby extracting stable heartbeat and respiration signals. the face tracking algorithm can also be expanded to multi-person tracking, i.e., more than two human faces can be monitored simultaneously to avoid a 'human traffic jam' in places of mass gathering such as airports. in summary, the feasibility of using irt to remotely sense multiple vital signs and to rapidly and accurately screen patients who are suspected of carrying infectious diseases has been demonstrated, and it appears that this is a very promising approach that will provide an alternative to conventional feverbased screening. the authors state that they have no conflicts of interest to declare. airport arrivals screening during pandemic (h1n1) 2009 influenza in new south wales, australia mass screening of suspected febrile patients with remote-sensing infrared thermography: alarm temperature and optimal distance analysis of ir thermal imager for mass blind fever screening modern approach to infectious disease management using infrared thermal camera scanning for fever in healthcare settings fever screening during the influenza (h1n1-2009) pandemic at narita international airport a novel screening method for influenza patients using a newly developed non-contact screening system an infectious disease/fever screening radar system which stratifies higher-risk patients within ten seconds using a neural network and the fuzzy grouping method multiple vital-sign based infection screening outperforms thermography independent of the classification algorithm a novel infection screening method using a neural network and k-means clustering algorithm which can be applied for screening of unknown or unexpected infectious diseases non-contact measurement of respiratory and heart rates using a cmos camera-equipped infrared camera for prompt infection screening at airport quarantine stations advancements in noncontact, multiparameter physiological measurements using a webcam dimension reduction-based penalized logistic regression for cancer classification using microarray data clinical tests: sensitivity and specificity characteristics of infectious diseases in hospitalized patients during the early phase after the 2011 great east japan earthquake: pneumonia as a significant reason for hospital care infectious diseases following natural disasters: prevention and control measures monitoring of influenza viruses in the aftermath of the great east japan earthquake this work was supported by a grant-in-aid for young scientists (grant number 16k16363) that was funded by the japanese ministry of education, culture, sports, science and technology. key: cord-259837-5tbdqzxr authors: kalcioglu, mahmut tayyar; cag, yasemin; kilic, osman; tuysuz, ozan title: may covid-19 cause sudden sensorineural hearing loss? date: 2020-09-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1468 sha: doc_id: 259837 cord_uid: 5tbdqzxr nan we thank to pietro d l et al for their comments on our recently published article (kilic et al., 2020) . in previous studies, viral infections have been reported to have an important role in the etiology of sudden sensorineural hearing loss (ssnhl) (cohen et al., 2014) . therefore, it is not unreasonable to think that covid-19, as a viral infection, may also cause ssnhl. moreover, recently, studies on the effects of sars-cov-2 virus on central and peripheral nervous systems have been published. some of these studies have reported guillain -barré syndrome (toscano et al., 2020) and impaired olfactory function (eliezer et al., 2020) to be related to sars-cov-2. another recently published study reported neurologic changes in 58 of 64 patients with covid-19 (helms et al., 2020) . when we observed an unexpected increase in ssnhl cases with no other symptoms in our ent outpatient clinics during the covid-19 pandemic, we thought that it might be related to covid-19. therefore, we investigated the possibility of sars-cov-2 infection in these j o u r n a l p r e -p r o o f patients. by using rt-pcr method, we detected the presence of sars-cov-2 in one of our 5 patients (kilic et al., 2020) . our study is the first in the literature to show that there may be a relationship between ssnhl and covid-19. the results of a recent study on the effect of covid-19 on hearing functions supports our hypothesis (mustafa, 2020) . the author reported that both transient evoked otoacoustic emissions and high frequency pure-tone thresholds amplitudes were significantly worse in the asymptomatic covid-19 pcr-positive patients group. undoubtedly, routine healthcare services are disrupted during the pandemic, so the association of ssnhl cases with covid-19 may have been gone unnoticed in healthcare institutions due to the increased workload. of course, in order to make a definitive diagnosis, studies that would demonstrate the presence of the virus in the relevant tissues, such as postmortem studies, are required. however, in the ongoing pandemic, we believe that every symptom should be taken into consideration and shared with the medical community. we believe that our article will increase awareness on this issue. thus, will encourage the design of large studies, in the regions with high prevalence of covid-19, as also suggested by pietro et al. viral causes of hearing loss: a review for hearing health professionals sudden and complete olfactory loss function as a possible symptom of covid-19 neurologic features in severe sars-cov-2 infection could sudden sensorineural hearing loss be the sole manifestation of covid-19? an investigation into sars-cov-2 in the etiology of sudden sensorineural hearing loss audiological profile of asymptomatic covid-19 pcr-positive cases barré syndrome associated with sars-cov-2 the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-302409-40ktyt5q authors: wang, jie; feng, haiting; zhang, sheng; ni, zuowei; ni, lingmei; chen, yu; zhuo, lixin; zhong, zifeng; qu, tingting title: sars-cov-2 rna detection of hospital isolation wards hygiene monitoring during the coronavirus disease 2019 outbreak in a chinese hospital date: 2020-04-18 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.024 sha: doc_id: 302409 cord_uid: 40ktyt5q objectives: the aim of this paper was to monitor the presence of sars-cov-2 among hospital environment surfaces, sewage, and personal protective equipment (ppe) of staffs in isolation wards in the first affiliated hospital of zhejiang university, china. methods: surfaces of objects were routinely wiped with 1000 mg/l chlorine containing disinfectant. air and sewage disinfection was proceeded routinely and strictly. hospital environmental surfaces and ppe of staffs in isolation wards were sampled using swabs. the sewage from various inlet and outlets were sampled. the respiratory and stool specimens of patients were collected. the respiratory specimens of staffs in the isolation wards were also sampled once a week. quantitative real-time reverse transcription pcr (qrt-pcr) methods were used to confirm the existence of sars-cov-2 rna. viral culture was done for the samples positive for sars-cov-2 rna. results: during the study period, 33 laboratory-confirmed patients were hospitalized in isolation wards in the hospital. none of sars-cov-2 rna was detected among the 36 objects surface samples and 9 staffs ppe samples in isolation wards. though the 3 sewage samples from the inlet of preprocessing disinfection pool were positive for sars-cov-2 rna and the sample from the outlet of preprocessing disinfection pool was weakly positive, the sewage sample from the outlet of the last disinfection pool was negative. all of the 5 sewage samples from various points were negative by viral culture of sars-cov-2. none of the respiratory specimens of staffs in the isolation wards were positive. conclusions: though sars-cov-2 rna of the sewage samples were positive from inlets of the sewage disinfection pool and negative from the outlet of the last sewage disinfection pool, no viable virus was detected by culture. the monitoring data in this study suggested that the strict disinfection and hand hygiene could decrease the hospital-associated covid-19 infection risk of the staffs in isolation wards. since december 2019, coronavirus disease 2019 emerged in wuhan city, then rapidly spread throughout china, and was also reported in other countries (benvenuto et al., 2020; huang et al., 2020; park et al., 2020; tian et al., 2020; xu et al., 2020; zhang et al., 2020) . the virus was subsequently renamed sars-cov-2 as it is similar to the coronavirus responsible for severe acute respiratory syndrome (sars-cov), a member of the subgenus sarbecovirus (beta-cov lineage b). the transmission of sars-cov-2 is associated with close contact to covid-19 patients and droplet secretions of those patients. according to a report from the china centers for disease control and prevention, up to february 24th 2020, 3387 medical staffs were confirmed with covid-19, of which were mainly occurred in january 2019 from hubei province (novel coronavirus pneumonia emergency response epidemiology, 2020; wang et al., 2020) . the occurrence of healthcare-associated infections might be closely related to pathogens contamination in the hospital environment (beggs et al., 2015 , chowell et al., 2015 . the outbreak of this novel virus placed challenges on hospital environmental hygiene. because of the covid-19 pandemic, the isolation wards in general hospitals have all been transformed into temporary infectious disease wards. in the past, several studies on environmental sampling have performed to identify the contamination in field-settings with sars or mers-cov (bin et al., 2016; otter et al., 2016) . though the data was limited, it appeared that the survival capacity of various human coronavirus was different (chan et al., 2011; van doremalen et al., 2013) . recently, sars-cov-2 rna has been detected from a door handle in a confirmed covid-19 patient's home by centers for disease control and prevention (cdc) in guangzhou, china. it was also reported that sars-cov-2 rna was detected in hospital environment in singapore . hence, comprehensive monitoring of hospital environmental hygiene during the outbreak of the pandemic is significant to ensure the safety of medical treatment and the quality of hospital infection control. in order to monitor the hospital environmental hygiene and evaluate the quality of hospital infection control, we reveal the sars-cov-2 rna data of environmental hygiene in the isolation wards of the first affiliated hospital of zhejiang university. the severe patients with covid-19 in zhejiang province were collected and hospitalized in the zhijiang campus, first affiliated hospital of zhejiang university, china. the zhijiang campus of the first affiliated hospital of zhejiang university was transformed into temporary infectious disease hospital. confirmed patients of covid-19 were hospitalized in the 3 isolation wards including one isolation intensive care unit (icu) ward and two general isolation wards. each isolation ward was separated into three parts and two passages. three zones including contaminated area, semi-contaminated area, and clean area. a contaminated area is a specifically designated area for patients of covid-19 and contaminated items such as patients' wastes. a clean area is a specifically designated area for non-contaminated items. patients should not enter the clean area. semi-contaminated area was set up between the contaminated area and the clean area. the items were potentially polluted can be placed in this area. doctor's offices were placed in this area. while two passages are a passage for medical staff and a passage for patients. buffer room is set up between a contaminated zone and a semi-contaminated zone. in each isolation ward, two buffer zones are set up for removing the staff ppes in accordance with the transmission features of covid-19. the suspected patients of covid-19 were nursed in single rooms, while the confirmed patients of covid-19 were cohorted in cubicles with bed spacing of not less than 1.2 meters. the isolation rooms were not under negative pressure because the isolation wards were reconducted temporarily. disinfection of indoor air in isolation wards of medical institutions refer to hospital air purification management code (ws/t 368-2012) by air disinfector based on plasma. visible contaminants on surfaces of treatment facilities and equipment including bed rails, nightstand, furniture, door handles and other household items, should be completely removed before disinfection. surfaces of objects were routinely wiped with 1000 mg/l chlorine containing disinfectant every 4 h in isolation icu ward and every 8 h in general isolation wards. preprocessing disinfection equipment were added before sewage drainage from the isolation wards into the final sewage disinfection pool. sodium hypochlorite was used for sewage disinfection. respiratory and stool specimens collected from all patients at admission were tested by real time polymerase chain reaction for sars-cov-2 rna. the respiratory specimens such as naso-vs. oropharyngeal swabs or sputum samples of staffs in the isolation wards were collected once a week and tested by real time polymerase chain reaction for sars-cov-2 rna. hospital environmental sampling and staff personal protective equipment (ppe) sites sampling during february 19th-24 th , 2020, we collected samples of the environmental surfaces in isolation icu ward and isolation wards, including the clean area, the semi-contaminated area, and the contaminated area. environmental surfaces were sampled by using classiqswabs (copan flock technologies, brescia, italy), and collected in universal transport medium (utm) containing hanks' balanced salt solution, bsa, hepes, amino acids, glycerin and so on. sewage from the isolation wards were collected from various inlet and outlet were sampling. front surface of n95 masks and gloves of staffs in isolation wards were also sampled using swabs and collected in utm. (table 1) . laboratory confirmation of the virus was performed using real time reverse transcription polymerase chain reaction using the sars-cov-2 nucleic acid detection kit (shanghai berger medical technology co., china) xu et al., 2020) . cycle threshold values, i.e., number of cycles required for the fluorescent signal to cross the threshold in rt-pcr, quantified viral load, with lower values indicating higher viral load. a sample was considered positive when the qrt-pcr ct value was 40. virus culture must be performed in a laboratory with qualified biosafety level 3 (bsl-3). samples were obtained and inoculated on vero-e6 cells for virus culture. the cytopathic effect (cpe) was observed after 96 h. detection of viral nucleic acid in the culture medium indicated a successful culture. during the period from february 19th to 24th, 2020, a total of 33 laboratory-confirmed covid-19 patients were hospitalized isolation ward in zhijiang campus, the first affiliated hospital of zhejiang university, china. among the 33 laboratory-confirmed covid-19 hospitalized patients, 9 intensive care patients were hospitalized in isolation icu ward including 7 patients with mechanical ventilation and 2 patients without mechanical ventilation. the other 24 patients were hospitalized in the other two general isolation wards. all the patients without mechanical ventilation were wearing surgical masks all the time in isolation wards. detection of sars-cov-2 rna among health-care settings, sewage, and staffs' ppe in routine cleaning and disinfection, the 36 samples of environmental surface in isolation wards including the clean area, the semi-contaminated area, and the contaminated area were all negative. front surface of n95 masks and gloves of staffs in isolation wards were also negative for sars-cov-2 rna (table 1) . three sewage samples from the inlets of preprocessing disinfection equipment were positive for sars-cov-2 rna (cycle threshold value 29.37, 30.58, and 32.42). after preprocessing disinfection, the sewage sample from outlet of preprocessing disinfection pool was weakly positive (cycle threshold value 33.55). the sewage sample from final outlet of the last sewage disinfection pool was negative. (table 1 ) however, all of the 5 sewage samples were negative by viral culture. patient a and b were hospitalized in isolation icu ward. the sampling of nightstands and bed rails were surrounding the patient a and b, respectively. during the study period, the respiratory and stool samples of patient a with mechanical ventilation were positive for sars-cov-2 rna with cycle threshold value 19.85 and 21.28 respectively. while, the respiratory sample of patient b without mechanical ventilation was positive for sars-cov-2 rna with cycle threshold value 28.37, but the stool sample negative for patient b. all of the staffs' respiratory specimens in the isolation wards were negative. the transmission of sars-cov-2 was reported to be associated with close contact to covid-19 patients and droplet secretions of those patients (zou et al., 2020) . stool specimens of covid-19 patients were positive for sars-cov-2, suggesting that viral shedding in stool might be a potential route of transmission which was also reported in sars previously (wang et al., 2005) . in recent studies, environmental sampling also has identified contamination in field-settings with sars-cov-2 . if sars-cov-2 transfers to hands or other equipment at a concentration above the infectious dose, it will initiate infection through contact with the eyes, nose or mouth by indirect contact. thus, an effective disinfection is very necessary for hospital infection control and medical staffs' protection. with the outbreak of covid-19 in china, the isolation wards in general hospitals have all been transformed into temporary wards in order to meet the standard of isolation wards in infectious disease hospitals. such temporary isolation wards might have many concerns. further environmental monitoring assessments are necessary. during sampling process in our study, a total of 33 laboratory confirmed patients with covid-19 were hospitalized in the isolate wards including one isolation icu ward and two general isolation wards. with routine cleaning and disinfection, none of sars-cov-2 rna was detected among object surfaces in isolation wards including the clean area, the semi-contaminated area, and the contaminated area. siegel et al. reported that medical ventilators might generate respiratory aerosols that have been associated with an increased risk of occupationally acquired infection among healthcare personnel (siegel et al., 2007) . we also detected the object surfaces such as bed rails and nightstands surrounding the covid-19 patients with or without mechanical ventilation. the two patients' respiratory specimens were both positive for sars-cov-2 rna, while the stool specimen of patient a with mechanical ventilation was positive for sars-cov-2 rna but that of patient b without mechanical ventilation was negative. the object surfaces closely surrounding the two patients with or without mechanical ventilation were all negative for sars-cov-2 rna. the sampling time was about 4 h after objects disinfection with 1000 mg/l chlorine containing disinfectant. it indicated that the current disinfection measure was effective in isolation wards in hospital. the negative sars-cov-2 rna results of the objects surfaces such as door handles, pda and gloves of staffs also suggested the effectiveness of the high hand hygiene compliance of staffs in isolation wards. also, sars-cov-2 rna was not detected among front surface of n95 masks of staffs in isolation wards. it also indicated that our staffs with ppe in the transformed isolation wards with current disinfection measure were in low risk of infection. in this study all the respiratory specimens of staffs in the isolation wards were negative. since sars-cov-2 rna was also detected in the stool specimen of patients with covid-19 in previous reports (yeo et al., 2020; young et al., 2020) , sars-cov-2 rna was also detected in sewage in our study. for sufficient disinfection of sars-cov-2, preprocessing disinfection equipment were added before the sewage drained into the last disinfection pool. though the sewage samples from the inlet of preprocessing disinfection equipment were positive for sars-cov-2 rna and the sample from the outlet of preprocessing disinfection was weakly positive, the sewage sample from the final outlet of the last disinfection pool was negative. in order to identify the viability of the sars-cov-2, viral culture was done among these sewage from various points. all of the sewage samples from various points were negative for viral culture. this finding also indicated that the sewage drained from the hospital could not lead to transmission of the sars-cov-2. this study also has several limitations. first, viral culture was not done among all of the 33 patients to demonstrate viability. second, due to operational limitations during an outbreak, sample size was small. third, the air was not sampled for sars-cov-2 rna detection in the study. further studies are required to confirm these preliminary results. in conclusion, the sars-cov-2 rna monitoring results of the hospital isolation wards demonstrated the routine disinfection measures of air, object surface and sewage in the hospital were sufficient and the hand hygiene of staffs was effective. though the transmission of sars-cov-2 is associated with close contact to covid-19 patients and droplet secretions of those patients, the strict disinfection and hand hygiene can decrease the hospitalassociated covid-19 infection risk of the staffs in isolation wards. this work was supported by the fund of zhejiang province medical and health science and technology project (2018ky388). this study was approved by the local ethics committees of the first affiliated hospital, college of medicine, zhejiang university. environmental contamination and hospital-acquired infection: factors that are easily overlooked the global spread of 2019-ncov: a molecular evolutionary analysis environmental contamination and viral shedding in mers patients during mers-cov outbreak in south korea the effects of temperature and relative humidity on the viability of the sars coronavirus transmission characteristics of mers and sars in the healthcare setting: a comparative study clinical features of patients infected with 2019 novel coronavirus in wuhan, china novel coronavirus pneumonia emergency response epidemiology t. the epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (covid-19) in china air, surface environmental, and personal protective equipment contamination by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) from a symptomatic patient transmission of sars and mers coronaviruses and influenza virus in healthcare settings: the possible role of dry surface contamination virus isolation from the first patient with sars-cov-2 in korea health care infection control practices advisory c. 2007 guideline for isolation precautions: preventing transmission of infectious agents in health care settings stability of middle east respiratory syndrome coronavirus (mers-cov) under different environmental conditions reasons for healthcare workers becoming infected with novel coronavirus disease 2019 (covid-19) in china concentration and detection of sars coronavirus in sewage from xiao tang shan hospital and the 309th hospital clinical findings in a group of patients infected with the 2019 novel coronavirus (sars-cov-2) outside of wuhan, china: retrospective case series epidemiologic features and clinical course of patients infected with sars-cov-2 in singapore the novel coronavirus (sars-cov-2) infections in china: prevention, control and challenges sars-cov-2 viral load in upper respiratory specimens of infected patients the authors have no conflicts of interest to declare. key: cord-316209-juvmabdq authors: rutayisire, erigene; nkundimana, gerard; mitonga, honore k.; boye, alex; nikwigize, solange title: what works and what does not work in response to covid-19 prevention and control in africa date: 2020-06-12 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.024 sha: doc_id: 316209 cord_uid: juvmabdq abstract since the emergence of the pandemic in december 2019 in wuhan, china, as of 10:00 cest, june 6, 2020, there have been nearly 6,663,304 confirmed cases of covid-19 including 392,802 deaths worldwide. in africa, as of june 2, 2020, a total of 152,442 covid-19 cases and 4334 deaths have been reported. the five countries with the highest commutative number of cases in africa are south africa, egypt, nigeria, algeria, and ghana. africa, together with the rest of world have had to swiftly undertake measures necessary to protect the continent from irreversible effects of the covid-19 pandemic that is claiming lives and destroying livelihoods. the lower number of covid-19 cases in most african countries is attributed to inadequate health systems, low-to-absent testing capacity, poor reporting system and insufficient number of medical staff. the covid-19 pandemic poses a great threat to most african countries from cities to rural areas and has created a strong demand on already scarce resources and requires an intense mobilization of additional resources to implement established emergency contingency measures. closure of borders and movements of people restrictions within the country as measures to prevent the spread of covid-19; this has resulted in the sector being adversely affected by the loss of income. cooperative prevention and control measures are one of the promising solutions to deplete the spread of covid-19 on the continent. since its emergence in december 2019 in wuhan, china, there have been nearly 6,663,304 confirmed cases and 392,802 deaths related to coronavirus disease as reported from 215 countries and territories (who situation report-138, 2020) . on 11 march 2020, the world health organization (who) had declared covid-19 a pandemic, pointing to the over 118,000 cases of the coronavirus illnesses in over 110 countries and territories around the world and the sustained risk of further global spread. the rapidly evolving covid-19 pandemic places a heavy burden on health care systems. this burden is projected to become worse in low and middle income countries already struggling with weak health-care systems, scarce financial resources as well as protective equipment, poor testing and treatment capacities, and lack of research funding (betsch et al.,2020) . low and middle income countries need enormous global support to prepare for impending crisis (the lancet, 2020) and identify where they can allocate more resources to prevent and control covid-19. as of 9 am eat 2 june 2020, a total of 152442 covid-19 cases and 4334 deaths have been reported in 54 african countries. this is about 2.5 of all cases reported globally. since the last brief on may 26 th from africa cdc, the number of covid-19 cases has increased by 32% (37096 cases), this shows the burden covid-19 could impose on african countries. as of june 2 nd , the five countries with the highest cumulative number of cases are as of south africa (34357 cases), egypt (26384 cases), nigeria (10578 cases), algeria (9513 cases), and ghana (8070 cases) (africa cdc, outbreak brief-20, 2020) . comparatively low positive cases of covid-19 in africa is attributed to low-to-absent testing capacity, poor reporting system, and insufficient number of medical staff. evidently, covid-19 poses a great threat to most african countries from cities to rural areas (lucero-prisno et al. 2020) ; it has created a strong demand on already scarce resources and requires an intense mobilization of additional resources to support local emergency contingency measures in compliance with who and africa cdc recommendations and directives. the africa continent, as with the rest of the world, continues to confirm additional cases of covid-19. up to now, the covid-19 has no effective treatment and there are no available vaccines and can spread from both asymptomatic and symptomatic cases. covid-19 is the type of infectious disease that is highly transmissible, crosses borders and threatens countries health j o u r n a l p r e -p r o o f 5 and global economy. patients with covid-19 especially those with comorbidities may develop severe disease and experience adverse outcomes creating additional burden to healthcare systems in place. that is why, the authorities specifically in africa have the duty to respond to this pandemic with effective and appropriate interventions, policies and messages. at present in order to protect citizens' health, most of the african countries have activated their national health emergency management committees, special committees on covid-19 response that are mostly chaired by ministers of health. as new evidence become available, african countries continue to share experiences and effective strategies in order to improve covid-19 prevention and control in solidarity. africa centers for diseases control and prevention (africa cdc), world health organization and other international agencies are providing support and guidance to many african countries in response to covid-19 pandemic. since the early stage of covid-19 in africa, many african countries have received facemasks, ventilators, test kits and other medical equipment from different countries and international agencies. specifically, africa cdc is providing guidelines on contact tracing, community social distancing, africa joint continental strategy for covid-19 outbreak and weakly scientific and public health policy updates (africa cdc: outbreak brief #20). african union has established africa taskforce for novel coronavirus (aftcom) as a continental platform to better coordinate all covid-19 prevention measures across the continent. through an established task force, africa cdc supports affected countries in surveillance by proving remote technical support to the african union member states (africa cdc, feb 2020). most african countries appreciated the importance of lockdown, closure of borders and restrictions on people's movement within the country as measures to prevent the spread of covid-19. the lockdown has ranged between 14-60 days in most african countries. as cases in the continent continue to rise, member states have continued to extend imposed public health measures including total lockdown in senegal, sierra leone, and zimbabwe. mandatory wearing of masks in public is also going on in botswana and rwanda. other member states allow partial reopening of the economy and/or schools including benin, botswana, cameroon, lesotho, djibouti, nigeria and burkina faso. but, precautionary measures, such as wearing facemasks, use of hand sanitizer and gloves while maintaining social distancing remain in place. in response to africa cdc recommendation to reduce the spread of covid-19, 43 african countries have closed their borders, 7 closed international air traffic, 2 imposed travel restrictions to and from specific countries and 3 imposed entry/exit restrictions. in addition, some african to protect vulnerable citizens' health, some african governments have allocated resources to cover their basic needs. for example, zimbabwe had budgeted over $ 600 million for vulnerable households under a cost transfer program for the next 3 months; rwanda and ghana took 7 initiatives of providing food and other primary needs to needy population hit hard by covid-19 pandemic. in namibia, the government initiated the emergency income grant (eig) amounting to n$562.0 million. the grant is a once-off payment of n$750.00 in cash grant per qualifying person, on the basis of a set of eligibility criteria properly defined for vulnerable people. it is estimated to benefit up to 739,000 namibians. countries commit to leave no solution unexplored to ensure a healthy recovery from covid-19 and pursue return to work strategies once the disease is under control. unfortunately, african countries are not complying at the same level to the covid-19 prevention and control measures. disparity in responses to the pandemic across africa countries are linked to the different timing in the start of the diseases, existing lack of adequate resources for the health care, poor public health systems and community ignorance. despite reported low case-fatality of covid-19, the pandemic is likely to cause more deaths in africa if the compliance to covid-19 prevention and control measures continues to be ignored as observed in some african countries. there is a growing concern that covid-19 could spread further and heavily hit the african continent (wafaa me., & justman j.,2020), due to the existing fragile health care and public health systems, inadequate health care infrastructure, lack of access to safe water and sanitation, lack of food safety and political instability. in africa, one factor that could mitigate covid-19 related mortality is its very young population demography; in fact, more than 50% of the african population is under the age of 20 years old. however, this group of people is also surrounded by many problems including poverty, food insecurity, illiteracy and unemployment among others. lockdown policies may put them at greater risk of getting covid-19, lack of access to food may force them not to stay home, oblige them to go out for survival and thereafter get infected and eventually die of covid-19. experience from asia, europe and usa showed that people with existing health problems are most vulnerable to severe cases of covid-19. the burden of health problems in africa is proportionately higher than the rest of the world. consequently, the higher prevalence of j o u r n a l p r e -p r o o f 8 malnutrition, anemia, malaria, hiv/aid, and tuberculosis in many african countries may coincide with and worsen the ongoing covid-19 pandemic prevention and control measures in africa. taking into account the technical advice from africa cdc, and who, most countries have taken covid-19 pandemic seriously; cases are identified, tested and treated coupled with contact tracing in many african countries. however, there is always a delay in contact-tracing where some patients are still found in the general population having tested positive or becoming extremely difficult to trace along with their contacts. despite the message of self-isolation and toll free number for those with covid-19 symptoms, people in some african countries still tend to disregard the symptoms until they become severely ill. this thus increases the risk to family members in contact and the community in general. it was observed that in some african countries, people are resisting to testing over quarantine fears. for example, kenyans are resisting or simply not turning up for covid-19 testing. the main reasons fronted for this behavior are that the residents are terrified of the prospect of being found to be infected, which in turn would mean being quarantined and self incurring all quarantine costs. this resistance greatly hinders africa governments planning and interventions. considering the existing economic conditions of african citizens, the costs of quarantine are supposed to be paid by the government. african countries are struggling to increase diagnostic capacity, improve infection prevention control (ipc) as well as manage confirmed cases as need arises. if the cases continue to increase, many african countries will not be able to manage those cases; there is a need for international cooperation to reduce the burden this disease will impose on african countries. with the spread of the disease, the pandemic is dismantling gains in the social-economic fabrics of all nations and societies, and it is exposing and deepening -further emphasizing the unsustainability of previously existing weaknesses, including poverty and inequality. some people in africa have resisted staying home policies mainly due to cultural and religious beliefs. measures to impose social and physical distancing have proven to be more challenging in african countries such as senegal and tanzania (world economic forum, march 2020). it was j o u r n a l p r e -p r o o f 9 proven that during covid-19 prevention and control measures, poor people are mostly affected. for example, people demonstrated in kenya and south africa due to lack of food and sent out a clear message that they prefer to die from covid-19 instead of hunger. moreover, compliance with recommended social distancing is still a problem in some places such as public markets, banks and refugee camps. in most public markets in africa, sellers are not concerned about the risk of getting covid-19, they are neither wearing masks nor using hand washing soap, water and hand sanitizers and sellers seem only to be interested in getting money from buyers. hence, we advise africa union member states to revisit their policies by allowing a small number of people, as it is implemented in namibia, to enter in such markets while others are waiting outside of the facility and keeping the social distancing of about 1.5 meter, providing hand washing facilities and hand sanitizers. there is also a need to continue to inform the public on the importance of adherence to social distancing measure to prevent and control covid-19 (lucero-prisno et al. 2020) . in order to ease the lockdown, african governments need to make sure that the spread of covid-19 is mitigated by ensuring that people comprehend the significance of social distancing as well as wearing facemasks. african countries are battling to augment diagnostic capacities, improve ipc as well as manage confirmed cases as need arises. if new reported cases persist, numerous african countries will be unable to handle them effectively. aggressive prevention measures are one of the strategies that africa should use to prevent more covid-19 cases and deaths in coming months. cooperative prevention and control measures are one of the promising solutions to deplete the spread of covid-19 on the continent. not needed monitoring behavioural insights related to covid-19 the lancet: covid-19 will not leave behind refugees and migrants covid-19) pandemic date of issue: 2 communique by the emergency meeting of africa ministers of health on the coronavirus disease outbreak "coordinated actions to prepare and respond to covid-19 infection in africa guidance on community social distancing during covid-19 outbreak scientific and public health policy update -31 recommendations for stepwise response to covid-19 outbreak/ health department republic of south africa: corona virus (covid-19 world economic forum: why sub-saharan africa needs a unique response to covid-19 current efforts and challenges facing responses to 2019-ncov in africa africa in the path of covid-19 who coronavirus disease (covid-19) situation reports none declared key: cord-320785-42p8292o authors: lobo, andréa de paula; cardoso-dos-santos, augusto césar; rocha, marli souza; pinheiro, rejane sobrino; bremm, joão matheus; macário, eduardo marques; oliveira, wanderson klébler de; frança, giovanny vinícius araújo de title: covid-19 epidemic in brazil: where we at? date: 2020-06-16 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.044 sha: doc_id: 320785 cord_uid: 42p8292o abstract objetive to analyze the trends of covid-19 in brazil in 2020 by federal units (fu). method ecological time-series based on cumulative confirmed cases of covid-19 from march 11 to may 12. joinpoint regression models were applied to identify points of inflection in covid-19 trends, considering the days since the 50th confirmed case as time unit. results brazil reached the 50th confirmed case of covid-19 in 11 march 2020 and, 63 days after that, on may 12, 177,589 cases had been confirmed. the trends for all regions and fu are upward. in the last segment, from the 31st to the 63rd day, brazil presented a dpc of 7.3% (95%ci= 7.2;7.5). for the country the adpc was 14.2% (95%ci: 13.8;14.5). the highest adpc values were found in the north, northeast and southeast regions. conclusions in summary, our results show that all fus in brazil present upward trends of covid-19. in some fus, the slowdown in dpc in the last segment must be considered carefully. each fus is at a different stage of the pandemic and, therefore, non-pharmacological measures must be applied accordingly. j o u r n a l p r e -p r o o f 4 of the epidemic (around 45-50 days after the 50 th case), compared other states, such as rondônia, sergipe and tocantins. some fus, such as pará, pernambuco, são paulo, paraná, and goiás showed a reduction in dpc in last segment in comparison with the previous one (table 1) . discussion: although all fus presented upward trends in the number of cumulative cases of covid-19, 18 out of 27 fus showed a reduction in the pace of the trend in the last segment. this may be related to the non-pharmacological measures adopted. 3, 4 despite the recent slowdown, 25 fus still present significant upward trends. some of them, such as amazonas, rio grande do south[adpl7], mato grosso, mato grosso do south [adpl8]and distrito federal even showed an increase in the dpc in the last segment. we highlight that the fus are at different stages of the epidemic, which can also explain those differences. even though the fus from the southeast region presented most of the confirmed cases, the highest adpc values were found in the northeast and north regions. this is particularly troublesome because these regions present the lowest human development indices, and the highest proportion of poverty and low education rates in some factors may have affected the inflections of the curves, such as the availability of diagnostic tests and the sensitivity of the epidemiological and laboratory surveillance system. 4,6 as we used publicly available data, analyses were performed using the notification date rather than the symptoms onset date, as well as the cumulative cases instead of incident cases. in future analyzes, other information will be added to investigate the inflections in the curve of a given territory, such as the validity of municipal or state decrees (lock-down this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. this work was developed with secondary data and approval by an ethics committee is not necessary. (36.9;58.8) 3-11 13.8*(12.7;14.9) 11-20 8.1*(7.2;9.0 • all of federative units in brazil shows a upward in accumulated cases of covid-19. • the highest increment were find in the north, northeast and southeast regions. • each federative unit in brazil is at a different stage of the covid-19 pandemic. covid-19 in latin america joinpoint regression program version 4.2.0 -april quarantine alone or in combination with other public health measures to control covid-19: a rapid review transmission dynamics of the covid-19 outbreak and effectiveness of government interventions: a data-driven analysis síntese de indicadores sociais: uma análise das condições de vida da key: cord-311026-mpr3xb2a authors: petersen, eskild; wasserman, sean; lee, shui-shan; go, unyeong; holmes, allison h.; abri, seif al; mclellan, susan; blumberg, lucille; tambyah, paul title: covid-19–we urgently need to start developing an exit strategy date: 2020-04-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.035 sha: doc_id: 311026 cord_uid: mpr3xb2a abstract aim the purpose of this perspective is to review the options countries have to exit the draconian “lock downs” in a carefully staged manner. methods experts from different countries experiencing corona virus infectious disease 2019 (covid-19) review evidence and country specific approaches and results of their interventions. results three key factors are important: 1. reintroduction from countries with ongoing community transmission; 2. the need for extensive testing capacity and widespread community testing, and 3. adequate supply of personal protective equipment, ppe, to protect health care workers. lifting social distancing is discussed at length. how to open manufacturing, construction and logistics. the opening og higher educational institutions and schools. the use of electronic surveillance is discussed. conclusion each country has to decide what is the best path forward. however, we can learn from each other and the approach is in reality very similar. with the sars-cov-2 pandemic passing one million ill people (1,521,252 confirmed cases and 92 798 reported deaths (who sit rep 10th april) most countries are occupied with controlling the outbreak. the economic consequences are enormous. the world trade organization (wto) estimate that "commerce could shrink up to 32% and warns against 30s-style protectionism" [wto 2020 ]. with no vaccine and no proven effective treatment, the tools available are limited to social distancing which include quarantine and travel restrictions. these tools are the same as were available during the black death due to plague in europe in the 13 th century although modern molecular diagnostics and electronic surveillance have modified them slightly. with no manual to follow most countries have taken a broad approach to slow down the spread of the infection, trying to "flatten the curve" to prevent overwhelming the health care systems by enforcing tight restrictions on population movements. this strategy has effectively "shut own" society and reduced economic activity by closing offices and manufacturing plants, closing schools, restricting mobility in public places, closing nonessential shops, restricting traffic (road, air and sea) and closing borders. this comes with a heavy socio-economic price, particularly in low-and-middle income countries with limited capacity to absorb prolonged national 'lockdowns'. many companies have or will file for government support or bankruptcy. unemployment is rapidly increasing, with devastating consequences on the lives of vulnerable populations, particularly in lowand middle-income countries (lmic). it is important to plan for the reactivation of society, restarting work and production, opening up for travels and education. no one knows the future and there have been speculations of "a second wave" which so far is conjectural but may well happen. a strategy or 'roadmap' for deescalating the enforced physical distancing based on epidemiological indicators is needed to inform citizens and policy makers. this review discusses from an epidemiological and medical point of view how strict isolation measures could gradually be lifted. the medical profession must lead the way out of the pandemic just as we shaped the response at the beginning. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. page 4 of 23 j o u r n a l p r e -p r o o f the post peak period -the "opening phase" what is the "post peak period"? there is no clear definition but most experts providing opinions to the media agree that having a plateau of cases or hospital admissions for two weeks signals that the transmission has stabilized and hospitals are able to treat all patients requiring hospitalization for covid-19 without resorting to crisis standards of care [zhang j et al. 2020 ]. this is the time when opening up society should be considered. however, because most of the population has not yet been exposed there are concerns that, with minimal but ongoing local transmission, new clusters might escape into the community triggering a second wave of infections [leung k et al., 2020 ]. in the "post peak" period it will be important to classify the epidemiological situation to increase the understanding of and target transmission and we suggest the following, adapted from the who [who 19 march 2020] (table 1) . there are important lessons from countries such as china and korea that managed to control the outbreak after experiencing a peak in the first-wave epidemic; taiwan [wang et al. 2020] and macau [lo et al. 2020 ] which managed to keep case counts low; and places where despite initial control there has been a resurgence such as singapore and hong kong. the experience from these countries point to three main challenges: 1. reintroduction from countries with ongoing community transmission (still in the outbreak phase) may initiate a new outbreak in the susceptible population. 2. the need for extensive testing capacity and widespread community testing to identify new cases as early as possible, coupled with effective contact tracing and isolation ability. 3. the importance of adequate supply of personal protective equipment, ppe, to protect health care workers. the outbreak has demonstrated how easily a respiratory infection can spread across borders. if countries open up for travel before widespread sars-cov-2 immunity there need to be interventions to reduce risk of transmission from travelers with few or no symptoms. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. page 5 of 23 j o u r n a l p r e -p r o o f 5 post-arrival quarantine has been applied effectively by south korea, but this is impractical and cannot be implemented in most countries. we believe that the international health regulation, ihr, an agreement between 196 countries including all who member states to work together for global health security, has an important role to play in enforcement of more targeted travel restrictions [ihr 2005 ]. under the ihr, using a mechanism similar to the yellow fever immunization certificate requirement, travelers could be asked to provide proof of previous infection, and therefore immunity, by having sars-cov-2 specific igg antibodies [petersen et al. 2020] . seronegative travelers could be asked undergo rapid testing (antigen or pcr in the airport pre-departure). however, rapid testing technologies are not yet available for routine implementation [petherick a et al. 2020 ]. in hong kong, truck drivers are required from the end of this week (9 th april 2020) to produce evidence of a "sars-cov-2 negative medical certificate" when they cross the hong kong -mainland border, as required by the chinese government; these ~10,000 drivers play an important role of ensuring that hong kong have food and commodities during the "lockdown". south korea imposed two weeks mandatory quarantine on all travelers entering the country from the 1st april; persons with previous infection as documented by positive serology are exempt. this is analogous to healthcare workers who are required to document immunity to varicella, measles, mumps, rubella and hepatitis b before working in most healthcare institutions. risk-based approaches to travel restrictions could also be considered. for example, travel restrictions could be eased between countries "past the peak" with local transmission at low levels. for instance, travels between germany and china could be opened under certain conditions that persons from third countries with high transmission rates would not be eligible for. another approach could be to open travel from countries with good surveillance systems, transparent reporting, and few local cases where risk of importing infected cases would be low. opening aviation routes would require agreement between the two countries for direct flights. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. page 6 of 23 j o u r n a l p r e -p r o o f 6 lifting the general restrictions on mobility and social distancing allowing business to open, opening schools and higher education institutions, staring manufacturing and allowing travel should be done after peak incidence. however, circulating virus has not disappeared, and resurgence remains a possibility. determining the rate at which mild disease is spreading in the community is critically important to inform shifts between containment and mitigation strategies. after de-escalation of enforced physical distancing by closing shops and work places, community-based symptom screening and testing must be made widely available to allow early identification of new cases. this will only be effective if supported by contact tracing, quarantine, and isolation that need supervision by public health authorities. in low-andmiddle income countries it will be essential to provide facilities for quarantine and isolation for people unable to safely do so in their homes. in the opening phase access to testing on broad indications must be available to all people to allow identification of new cases and clusters as early as possible. this would ideally be supported by point of care tests that are accurate and reliable. there should also be strong systems of surveillance for influenza-like illness, mortality rates, and sick leave. public health authorities must be properly staffed and equipped. a recent study from california testing patients with respiratory symptoms found that 11% of influenza-negative were sars-cov-2 pcr positive [zwald ml 2020] and such testing at sentinel sites is an important tool to keep track of community transmission. thus, public health capabilities for case identification and isolation must be expanded probably permanently; tools can include physical inspection or use of electronic devices, such as mobile phone-based surveillance and point of care tests as used in taiwan, korea and oman, summarized in table 3. the examples from korea, singapore and hong kong show that the virus will re-emerge if strict control measures are relaxed. the closure of all social activities and confining people at home has a profound effect on the economy and should only be maintained until other, an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. containment efforts could be focussed on populations at highest risk from infection, including people over 65 years old, people living in care institutions, and those with chronic medical conditions. these groups would need to be identified and supported to restrict their movements and practice social distancing for a longer period than the rest of society. communications about such an approach will be critical as the public currently has a strong negative attitude towards any mention of "herd immunity". during times of eased restrictions working from home -"teleworking" -should still be encouraged, and social gatherings discouraged. strategies to reduce workplace transmission include daily declarations of being symptomfree by all staff members, and where feasible, screening of staff by rt-pcr or even serology immediately after lifting of enforced quarantine, but the need to screen everyone at a work place before it opens up must be determined individually. this may be particularly important in higher risk industries such as the hospitality sector (tourists and hotels) and aviation or others with high degrees of interaction with vulnerable populations. the occupational health service will be important when manufacturing and construction industries open to keep a very close surveillance on employees and test and quarantine anyone with symptoms pending test results. similarly to targeted travel restrictions, opening up shops, offices, school and factories could be preceded by rt-pcr testing of asymptomatic or oligosymptomatic persons and/or introduction of widespread serological testing to confirm immunity prior to removal of individual quarantine. this would require massive mobilisation of resources and is unlikely to be feasible in lmics in the short term. it is critical to have communities as partners understanding the need for restriction even while some parts of society start working again. the higher the buy-in and quality of response in every locality, the better the outcome. universal masking has been proposed as an additional strategy for reducing community transmission. a surgical masks may reduce risk of community transmission from infected people [leung cc et al. 2020; chan kh et al. 2020 ]. this appears to have been effective in an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. page 8 of 23 j o u r n a l p r e -p r o o f 8 countries such as taiwan and south korea and parts of italy where mandatory mask wearing was implemented, although independent impact is difficult to assess. the who has recently stated that "the use of a medical mask can prevent the spread of infectious droplets from an infected person to someone else and potential contamination of the environment by these droplets" [who 2020e 6 april] and opening workplaces and ask employees to wear a face mask -surgical mask or equivalent -for two weeks after opening is an option which must be discussed with the occupational health service. lombardy in italy imposed mandatory face masks in public places [the guardian 2020] . we do not know if this will prevent person-to-person spread to the same extent as the closure of shops, factories, educational institutions and offices, but it make sense that masks (including non-medical) will reduce expulsion of large infectious droplets as stated by the who, thus reducing the risk of transmission in public spaces. in china, shops, restaurants, bars, and offices are opening. manufacturing activity is picking up and traffic starts to flow. three-quarters of china's workforce was back on the job as of 24 march, according to one company's estimate. wuhan, where the covid-19 pandemic originated, is lagging, as is the rest of hubei province-but even there, the lockdown was lifted the 8th april [normille d 2020]. the impact of this has yet to be determined. covid-19 clusters much more in families and households and social contacts of those households (fan j et al. 2020 ). more granular geographical information is needed for effective contact tracing, for instance using geographical information systems (gis). the lesson from south korea is that tracking of cases and contacts via modern digital technology to apply focused testing can control community transmission without enforced distancing [korean cdc 2020] . after identifying a case, contacts will be asked to self-quarantine and monitored by appropriate digital technology. random sampling would help to estimate the number of mild or asymptomatic cases and inform about the true attack rate in the population. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. a well-established and strong core program of infection prevention and control within the healthcare system is central to preparedness and responsiveness. it will also need to be maintained as a priority in the recovery phase of healthcare systems and national exit strategies. as the number of covid-19 inpatients diminishes and the proportion of inpatients that are covid-19 naïve rises again, the likelihood of potential nosocomial infection may increase. it is important that there are established hospital surveillance systems that can capture nosocomial infections rapidly and prevent the generation of hospital outbreaks and further waves of transmission. hand hygiene and environmental hygiene must be considered as underpinning priorities in protecting healthcare staff, and efforts must be made to promote social distancing in health care settings. the sars epidemic in hong kong demonstrated how vulnerable front line health care workers (hcws) are. protecting hcws is a major task and sufficient personal protective equipment (ppe) must be available [cheng vcc et al. 2020 ]. the protection of hcws and support staff is critical, and the resilience of healthcare systems is dependent on sustaining their safety and their trust. in covid-19 in comparison to sars, particular attention is needed to ensure that hcws seeing individuals at the earliest stages in the disease are also well protected, this would include those working in the community and in residential and care homes. ppe guidelines for healthcare systems need to be clearly communicated, understood, supported by staff and based on best evidence. however, the ppe recommended in any guidance must have the necessary supporting supply chain well defined and clearly mapped, along with the appropriate logistics and the capacity to maintain this. without continuous adequate, appropriate ppe provision for hcws and support staff, their sustained commitment and trust required for an effective exit strategy may be lost [cheng vcc et al. 2020; who ipc 2020] . up to the 27 th march, singapore had reported a total of 683 cases with 2 deaths. the ministry of health (moh) had developed a local case definition already by the 2 nd of january 2020 and sars-cov-2 real-time polymerase chain reaction (rt-pcr) laboratory testing capacity was scaled up rapidly to all public hospitals in singapore to handle 2,200 tests a day. all contacts were assessed by telephone for fever or respiratory symptoms by public health officials during the quarantine or monitoring period, thrice daily for close contacts and once daily for contacts at lower risk. in late january 2020 the following groups were tested for sars-cov-2: 1) all hospitalized patients with pneumonia (later expanded to include patients with pneumonia evaluated in primary care settings); 2) icu patients with possible infectious causes as determined by the physician; 3) patients with influenza-like illness at sentinel government and private primary care clinics included in the routine influenza surveillance network; and 4) deaths from possible infectious causes [ng y et al. 2020 ]. despite the city state's strict contact-tracing, quarantining and travel restrictions, a second wave of infections from returning residents and local transmissions saw cases spike from 100 to 1,000 in one month (scmp 3 rd april). the initial part of the second wave of infections involves singapore residents returning from countries such as the united states and britain. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. page 12 of 23 j o u r n a l p r e -p r o o f 12 the second wave also includes an increasing number of locally transmitted infections and cases with no known links to confirmed patients. in response to the second wave, the city state introduced stricter social distancing measures, barring the entry of all travellers closing bars and nightlife, and eventually introducing a strict lockdown in early april 2020 with schools, non-essential shops, places of worship etc. closed for a month as locally transmitted cases routinely exceeded a hundred a day. in hong kong, the first imported case of covid-19 was reported on 23 jan. 2020, two days before the lunar new year. from the last week of january 2020 the government had ordered closure of schools while most borders with mainland china were closed from the first week of february. between february and april control measures were stepped up. ordinance (cap 599), compulsory quarantine and social distancing orders became enforced. quarantine covers all people including local citizens entering hong kong. social distancing regulations include prohibition of gathering of more than 4 persons in public areas, restriction of number of customers and the occupancy of catering premises, closure of amusement game centres, bathhouses, fitness centers, bars and other entertainment places. there is no legal restriction on workplaces but the government has, since late january, mandated work-from-home arrangement for civil servants. however, vacation of workplaces affected not only the 170,000-strong government staff-force but also employees of statutory bodies, non-government organizations as well as major businesses. as of 9 april, 974 confirmed cases of sars-cov-2 infection were reported in the 7-million population city, with 4 deaths [government of hong kong 2020]. some 60% were imported cases or their contacts while local transmission especially dormitories with migrant workers accounted for the rest. over half of the non-imported cases could be traced back to their close contacts with reported local cases. there was marked increase of daily reports from less than 10 in january/february to 20-60 since the second half of march, which was attributed to the return of local citizens following acceleration of the european outbreaks, and the scaling up of testing. the main local transmission clusters had occurred in a religious worship area and social activities including dinner gatherings and entertainment bars. transmission linked to contacts in workplace has so far been uncommon. universal masking an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. page 13 of 23 j o u r n a l p r e -p r o o f 13 in public areas and on public transport is a common sighting, and in fact forms part of the general hygiene advice. such practice is required by law for staff and people patronizing catering premises, as stipulated in the newly enacted legal regulation. while the epidemic appeared to be less severe than other cities/countries in the region, restrictions have continued to be tightened to guard against major outbreaks. taiwan enhanced covid-19 case finding by proactively seeking out patients with severe respiratory symptoms (based on information from the national health insurance (nhi) database who had tested negative for influenza and retested them for covid-19 found of 113 cases. the toll-free number 1922 served as a hotline for citizens to report suspicious symptoms or cases in themselves or others; as the disease progressed, this hotline has reached full capacity, so each major city was asked to create its own hotline as an alternative. it is not known how often this hotline has been used. the government addressed the issue of disease stigma and compassion for those affected by providing food, frequent health checks, and encouragement for those under quarantine. this rapid response included hundreds of action items. taiwan citizens' household registration system and the foreigners' entry card allowed the government to track individuals at high risk because of recent travel history in affected areas. those identified as high risk (under home quarantine) were monitored electronically through their mobile phones. on january 30, the nha database was expanded to cover the past 14-day travel history for patients from china, hong kong, and macau. on february 14, the entry quarantine system was launched, so travelers can complete the health declaration form by scanning a qr code that leads to an online form, either prior to departure from or upon arrival at a taiwan airport. a mobile health declaration pass was then sent via sms to phones using a local telecom operator, which allowed for faster immigration clearance for those with minimal risk. this system was created within a 72-hour period. on february 18, the government announced that all hospitals, clinics, and pharmacies in taiwan would have access to patients' travel histories. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. south africa is an upper-middle income economy with a population of approximately 59 million people and one of the highest inequality rates in the world. critical concerns are the large population of people living in densely populated peri-urban areas with poor social circumstances plus the high national prevalence of hiv and tb, which may interact with sars-cov-2 to cause more severe disease. in addition, south africa's health services are already overburdened with limited capacity to absorb a large influx of covid-19 patients. the first case of covid-19 was detected on 5 march 2020 in a group of travelers from italy and the initial period of the epidemic was limited to imported cases and their contacts, occurring within a specific demographic of more middle class and relatively younger people. the government responded rapidly, announcing a national state of disaster on 15 march after 61 confirmed cases had been reported with evidence of local transmission (figure 2 ). this initial public health response included travel bans from countries with high levels of community transmission and 14-day mandatory quarantine for all returning travelers from those countries; school closures; cancellation of gatherings of more than 100 people; and expanding testing and isolation capacity. one week after these measures were implemented, and after case numbers had grown six-fold to 402 cases, a strict national 3week lockdown beginning 26 march was initiated, which prohibited all movement for citizens not involved in designated essential services "except under strictly controlled circumstances, such as to seek medical care, buy food, medicine and other supplies or collect a social grant." despite the profound impact of the lockdown on an already tenuous economy -estimated reduction in growth by 2.6% translating into ~9% contraction of national gdp -the president announced a 2-week extension on 9 april, following an apparent reduction in the average daily infection rate from 42% to 4%. critical challenges for transitioning to a risk-based containment strategy in south africa include limited testing capacity -currently 75,000 tests have been performed; matching the per-capita testing of south korea would require 400,000 tests -and lack of infrastructure to implement contact tracing and isolation for people living in dense peri-urban environments. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. each country has to decide how to open up society for work and social activities. a study comparing health care systems in hong kong, singapore and japan had three important conclusions [legido-quigley et al. 2020 ]. the first is that "integration of services in the health system and across other sectors amplifies the ability to absorb and adapt to shock". the second is that "the spread of fake news and misinformation constitutes a major unresolved challenge". finally, "the trust of patients, health-care professionals, and society as a whole in the government is of paramount importance for meeting health crises". while the surge of cases in these three countries may have altered the analysis somewhat, the general principles still apply. this is a new infection spreading in a nonimmune population and we have no manual -yet we have to take decisions. measures that can be used are summarized in table 4. as each country chooses its own path, we can learn from each other to determine the optimum approach that works in our setting. funding. the study received no funding table 2 . a reopening of society should be staged according to the local situation restrictions lifted for a specific sector of the society. could be schools, could be certain manufacturing industries, construction industry. could be limited to low endemic areas only. observe for 2 weeks, monitor hospital admissions, perform testing at sentinel sites and all persons with upper and lower respiratory tract infections. extend opening of manufacturing and construction industries open public transport but request face mask in public spaces open schools in more areas open international travels from selected countries, quarantine arrivals from high endemic countries or perform rapid dna test on arrival observe for 2 weeks, monitor hospital admissions, perform testing at sentinel sites and all persons with upper and lower respiratory tract infections. open small shops and restaurants provided social distancing is maintained. open international travels from selected countries, quarantine arrivals from high endemic countries or perform rapid dna test on arrival. observe for 2 weeks, monitor hospital admissions, perform testing at sentinel sites and all persons with upper and lower respiratory tract infections. open up for mass gatherings like football matches, religious gatherings etc. . . . . table 3 . generic electronic surveillance system. the system use information from mobile phones or bracelets. the system is linked to a national electronic surveillance system and to the civil identification number and can be shared with other stakeholders such as police or public prosecution. an "isolation enforcement system" can provide supervision of location of persons in isolation or quarantine outside institutions. isolation tracking app isolation compliance crowdsensing when people in quarantine move out of the isolation facility mobile phone and/or bracelet app self reporting and symptoms analysis self reporting questionnaires translation and language support the bracelet is for a single-use purpose that makes it very cost-effective and will be able to measure the body temperature the system will allow authorities to supervise compliance with quarantine and isolation anti-temper 12-month battery life perform contact history by linking geographical location of sim card or bracelet risk assessment according to the number of people quarantined or isolated in a specific geographical location. an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. table 4 . principles can help countries to plot a way out of the shutdown. 1. consider easing restrictions when the case count has decreased after the peak, has been stable for 2 weeks and the hospitals can cope with the number of serious cases. cases must be staged into imported, linked to known clusters and cases and unknown source. 2. expand testing for new and past infections by setting up sentinel testing sites, introduce testing stations in the community providing diagnostic tests to everyone with compatible symptoms and serological testing for surveillance of population immunity. introduce point-of-care (poc) testing when validated tests become available. 3. consider testing employees with nucleic acid tests and/or antibody test prior to return to work to find silent cases and recovered persons. this can be applied to schools also. in collaboration with the occupational health service establish sustainable workplace policies emphasizing infection control. 4. consider imposing the use of surgical or non-medical face masks whenever outside the household to reduce risk that persons with an unrecognized infection will contribute to transmission. this must be an adjunct to other ongoing social distancing interventions and hand hygiene. 5. continue to impose quarantine on arriving passengers from countries with active outbreaks. aim to develop a travel certificate for people with documented immunity with sars-cov-2-specific antibodies to be exempt from quarantine rules. 6. maintain strong infection prevention measures in all health care institutions 7. the sarc-cov-2 virus will most probably be in our societies for a long time until we have a vaccine. flare ups, small outbreaks and clusters is expected and thus the public health care system must be developed to take care of new cases, rapidly perform case and contact follow up and ensure quarantine. thus, a permanent upgrade of the public system is needed. covid-19 epidemic: disentangling the re-emerging controversy about medical facemasks from an epidemiological perspective escalating infection control response to the rapidly evolving epidemiology of the coronavirus disease 2019 (covid-19) due to sars-cov-2 in hong kong epidemiology of 2019 novel coronavirus disease-19 in gansu province, china, 2020. emerg infect dis. 2020;26:6. government of hong kong lombardy insists on face masks outside homes to stop covid-19. angela giuffrida in orvieto and peter beaumont impact of school closures for covid-19 on the us healthcare workforce and net mortality: a modelling study middle east respiratory syndrome coronavirus outbreak in the republic of korea disease control and prevention. the updates of the covid-19 in the republic of korea epidemiology and case management team. contact transmission of covid-19 in south korea: novel investigation techniques for tracing contacts guideline for covid-19 response interrupting transmission of covid-19: lessons from containment efforts in singapore are high-performing health systems resilient against the covid-19 epidemic? mass masking in the covid-19 epidemic: people need guidance first-wave covid-19 transmissibility and severity in china outside hubei after control measures, and second-wave scenario planning: a modelling an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. impact assessment. the lancet 2020 evaluation of sars-cov-2 rna shedding in clinical specimens and clinical characteristics of 10 patients with covid-19 in macau evaluation of the effectiveness of surveillance and containment measures for the first 100 patients with covid-19 in singapore can china return to normalcy while keeping the coronavirus in check? the korean middle east respiratory syndrome coronavirus outbreak and our responsibility to the global scientific community covid-19 travel restrictions and the international health regulations -call for an open debate on easing of travel restrictions developing antibody tests for sars-cov-2 coronavirus singapore: 100 to 1,000 infections in one month. what happened? 3 rd the government of the republic of korea. tackling covid-19. health, quarantine and economic measures: korean experience response to covid-19 in taiwan: big data analytics, new technology, and proactive testing operational considerations for case management of covid-19 in health facility and community. interim guidance who situation report-72. 1 st advice on the use of masks in the context of covid-19. interim guidance. geneva 6 th coronavirus disease (covid-19) technical guidance: infection prevention and control / wash. collection of documents an evaluation version of novapdf was used to create this pdf file trade set to plunge as covid-19 pandemic upends global economy evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside hubei province, china: a descriptive and modelling study rapid sentinel surveillance for covid-19 table 1. classification of new cases during surveillance in the imported, i.e. likely infections abroad b. part of known cluster, or contact to known case c an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice all authors contributed equally to the text.an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice.page 16 of 23 j o u r n a l p r e -p r o o f key: cord-257265-lkzytud0 authors: zheng, fang; zhou, yanwen; zhou, zhiguo; ye, fei; huang, baoying; huang, yaxiong; ma, jing; zuo, qi; tan, xin; xie, jun; niu, peihua; wang, wenlong; xu, yun; peng, feng; zhou, ning; cai, chunlin; tang, wei; xiao, xinqiang; li, yi; zhou, zhiguang; jiang, yongfang; xie, yuanlin; tan, wenjie; gong, guozhong title: sars-cov-2 clearance in covid-19 patients with novaferon treatment: a randomized, open-label, parallel group trial date: 2020-08-03 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.053 sha: doc_id: 257265 cord_uid: lkzytud0 background: the anti-viral effects of novaferon, a potent antiviral protein drug on covid-19 was evaluated in laboratory, and in a randomized, open-label, parallel group trial. methods: in laboratory, the inhibition of novaferon on viral replication in cells infected with sars-cov-2, and on prevention of sars-cov-2 entry into healthy cells was determined. antiviral effects of novaferon in covid-19 patients with treatment of novaferon, novaferon plus lopinavir/ritonavir, or lopinavir/ritonavir were evaluated. the primary endpoint was the sars-cov-2 clearance rates on day 6 of treatment, and the secondary endpoint was the time to sars-cov-2 clearance. results: novaferon inhibited the viral replication (ec(50) = 1.02 ng/ml), and prevented viral infection (ec(50) = 0.10 ng/ml). results from the 89 enrolled covid-19 patients showed that both novaferon and novaferon plus lopinavir/ritonavir groups had significantly higher viral clearance rates on day 6than lopinavir/ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053). median time to viral clearance were 6 days, 6 days, and 9 days for three groups respectively, a 3-dayreductionin both novaferon and novaferon plus lopinavir/ritonavir groups compared with lopinavir/ritonavir group. conclusions: novaferon exhibited anti-sars-cov-2 effects in vitro and in covid-19 patients. these data justified the further evaluation of novaferon. trial registration number: number chictr2000029496at the chinese clinical trial registry (http://www.chictr.org.cn/). the deadly pandemic of covid-19 caused by the infection of a novel coronavirus, sars-cov-2, represents a major health challenges around the world(who 2020; zhu et al., 2020; lu et al., 2020; wu et al., 2020) .the current failure on the containment of partially due to the lack of effective antiviral drugs for covid-19. such antiviral drugs, if administrated to early stage patients or to patients with mild and moderate illness, are reasonably expected to speed up the viral clearance. as a consequence, complete clearance of sars-cov-2 will lead to either the earlier recovery or to the reduction of the severe illness. in addition, the elimination of viral shedding following the viral clearance inpatients would also help to reduce viral transmission. given the immediate availability and established safety profiles, approved antiviral drugs for other indications were repurposed in order to find effective anti-sars-cov-2 drugs in the shortest time possible. (zhou et al.,2020) .however, none of the tested or recommended antiviral drugs has been proved effective yet. most published findings for the antiviral treatment of covid-19 were based on the individual case reports or cellular antiviral results holshue etal.,2020) .despite the lack of convincing evidence, lopinavir/ritonavir was quickly selected and recommended as an antiviral drug for covid-19 in china since january. so far, only limited observations of lopinavir/ritonavir for coronavirus in sars patients were reported (chu et al.,2004) .a recently completed trial of lopinavir/ritonavir j o u r n a l p r e -p r o o f in patients with severe covid-19 generated disappointed outcomes and revealed no significant antiviral effects (cao et al.,2020) .health care workers have to rely on the supportive and symptomatic treatments to manage covid-19 patients. given the daily increase of confirmed covid-19 cases and mortality, it is even more critical than two months ago to find antiviral drugs with efficacy supported by data from randomized clinical trials in covid-19 patients (xu et al., 2020; zhang et al.,2020) . novaferon as a novel antiviral protein drug which has been approved for treatment of chronic hepatitis b in china and exhibited broad-spectrum antiviral properties (unpublished data, available on requests) became an obvious candidate to be considered as a potential antiviral drug for covid-19.novaferon molecule is a non-natural protein consisting of 167 amino acids. according to the published information in a us patent (us 7, 625, 555 b2) , this novel protein molecule was created by modified dna shuffling technology using cdna sequences of 12 human interferon subtypes as models, and named as novaferon by its inventors (wang et al., 2011) .in addition to the human interferon-like physiological functions, novaferon exhibits better antiviral activities that are at least 10 times more potent than human interferon alpha-2b (li et al.,2014) .novaferon has been shown to enhance and improve the negative conversion of serum hbeag in clinical studies (daxianet al.,2015) , and in april 2018, was approved in china for treatment of chronic hepatitis b by former cfda (chinese food and drug administration). novaferon protein's non-proprietary name was temporarily defined as "recombinant cytokine genederived protein injection" by chinese pharmacopeia committee, and the recommended international non-proprietary name (rinn) by who is not available yet. for convenience purposes, novaferon was used as the drug name in our study. in the present study, we primarily attempted to observe the antiviral effects of novaferononcovid-19. we first determined whether novaferon was able to inhibit j o u r n a l p r e -p r o o f sars-cov-2 at cellular level, and subsequently conducted a randomized, open-label, parallel group trial to explore the antiviral effects of novaferon in covid-19patients by observing the sars-cov-2 clearance rates. the primary endpoint was the sars-cov-2 clearance rates on day 6, and the secondary endpoint was the median time tosars-cov-2 clearance after starting antiviral treatment. as a popular and recommended antiviral drug for covid-19 in china, lopinavir/ritonavir was included in this study to serve as a control for comparison. novaferon is a non-naturally existing protein molecule that is produced by recombinant technology via inserting a 498-nucleotides cdna into e. coli. the gene sequence (cdna) encoding novaferon protein molecule was created on the basis of modified dna shuffling technology to mimic the natural evolution of genome with intentions to invent novel protein molecules that have enhanced natural functions of the model proteins. in brief, cdna sequences of over 12 human interferon subtype genes were selected as the model genes for dna shuffling. these model cdna sequences were cut into fragments by enzymes and then repeatedly amplified to induce randomized nucleotide-mutation of the cdna fragments. the mutant cdna fragments in the reaction system randomly and spontaneously connected with each other to form a huge mutant cdna library. the clones of the newly formed cdna sequences that encoded protein molecules with the broadspectrum, enhanced antiviral and anti-proliferation activities were then screened and selected via a proprietary protein-screening method (high-efficient protein functional screen system). after screening more than 100000 cdna clones, a novel protein molecule has been identified to exhibit the enhanced potency against virus and tumor cells, and to possess the broad-spectrum antiviral and anti-proliferation properties as well. this novel j o u r n a l p r e -p r o o f protein molecule was named as novaferon subsequently. novaferon is encoded by 498 nucleotides and composed of 166 amino acids with the following amino acid sequence: cnlsqthslgskrtlmllaqmgkislfsclkdrhdfefpqeefdgnqfqkaqais vlheliqqtfnlfstkessaawdeglldkfrtelyrqlndleacmmqevgveet plmnadsilavkkyfqritlylmekkyspcawevvrveimrslsfstnlqkrlr gkd. as a non-naturally occurring protein, novaferon is not suitable to be classified according to the classification terms of human interferon subtypes. the nucleotide and amino-acid sequences of novaferon are 89% (445/498) and 81% (135/166) homology to human interferon α-2b which exhibit the best antiviral activities among all human interferon subtypes (uspto patent: us 7,625,555 b2) (wang et al., 2011) . novaferon drug used in this trial was manufactured in qingdao city of shandong province by genova biotech (qingdao) company limited. we further observed whether the previous treatment of vero e6 cells with novaferon protected the cells from viral entry through exposure of the pre-treated cells to sars-cov-2 later. detailed operation procedures were identical to the above description, except that the step orders were changed to allow the observation of the preventive effects of novaferon. briefly, blank vero e6 cells were incubated with series concentrations of novaferon for 2 hours, and the supernatants containing novaferon were then removed. the pre-treated vero e6 cells were exposed to sars-cov-2 by incubation with c-tan-ncov wuhan strain 01 (100pfu) for 2 hours, and the supernatants containing sars-cov-2 were then removed. fresh medium was added, and the cells were incubated for 48 hours. 100 j o u r n a l p r e -p r o o f μl of supernatants were taken from each well, and the total viral rna in the supernatants was measured using the same methods described above. the ct number obtained from vero e6 cells without pre-treatment of novaferon was considered as 100%, and the decreased ct numbers obtained from the pre-treated vero e6 cells with various concentrations of novaferon were used to calculate the inhibition percentages. the preventive effects of novaferon were then determined by observing the viral rna reduction in the cells pre-treated with novaferon. the ec50 of novaferon for the observed preventive effects was decided accordingly. sars-cov-2 virus nucleic acids were detected by rt-pcr using slan-96p automatic medical pcr analysis system. the sars-cov-2 nucleic acid detection kit was obtained from sensure biotechnology co. ltd ( hunan province, china ) , which has been approved for clinical test of sars-cov-2 by nmpa (national medical products administration). the lowest detection limit (sensitivity)of this rt-pcr assay kitwas200 copies of sars-cov-2rna in specimens. the specificity of this rt-pcr assay kit was determined by the failure of detecting viral rna (cross-reaction) in specimens containing other coronaviruses, rotavirus, astrovirus, and adenovirus et al. procedures of the tests strictly followed the protocol of the kit. samples from nasopharyngeal swab were collected in accordance with the standard procedures of the new coronavirus infection pneumonia laboratory test guide. fam (orf-1ab region) was used as fluorescent detection channel, and rox (n gene) channels were used to detect the sars-cov-2 nucleic acids, while hex channel was used as the internal standard. cycle parameter steps were in the following order: 1)reverse transcription at 50℃ for 30 minutes for 1 cycle; 2) pre-denaturation of cdna at 95℃ for 1 minute for 1 cycle; 3) j o u r n a l p r e -p r o o f denaturation at 95℃ for 15 seconds, and annealing, extension and fluorescence acquisition at 60℃ for 30 seconds for 45 cycles. 4) cooling at 25℃ for 10 seconds for 1 cycle. positive results were determined by comparing between the ct numbers of the testing samples and the standard ct number that was 40 in this assay. the study was originally designed as a multi-center study across hospitals in changsha city and in other cities of hunan province, china. however, per government order, all patients from hospitals in changsha city had to be relocated to the first hospital of changsha, a designated treatment center for all covid-19 patients in changsha city, and hospitals in other cities of hunan province were not able to participate due to various reasons. the study was changed to a single center study. this study was approved by the ethics committee of the first hospital of changsha (file number kx-2020002) and was conducted at the hospital. the study was also registered at the chinese clinical trial registry (http://www.chictr.org.cn/), number chictr2000029496. hospitalized covid-19 patients with confirmed sars-cov-2 detection, clinically classified as moderate or severe, at the age over 18 years, and without comorbidity of severe heart, lung, brain diseases, were eligible for enrolling into this study. moderate patients were defined as "patients with fever, symptoms of respiratory system and pneumonia changes in ct images, and severe patients were defined as "patients with any of the following: ① respiratory distress, respiratory frequency ≥30/minute;② under rest status, arterial oxygen saturation (sao2)≤93%;③arterial partial pressure of this was a randomized, open-label, parallel group study. patients eligible for the study were assigned, in a 1:1:1 ratio, to novaferon, novaferon plus lopinavir/ritonavir, or lopinavir/ritonavir group. a sas generated simple randomization schedule was prepared by a statistician not involved in the trial. based on the sequence that patients enrolled into the study, the patients were assigned to a treatment group which was implemented by a research assistant. informed consents were obtained from all enrolled patients. antiviral effects were assessed on day 3, day 6, and day 9 after starting drug administration. samples of nasopharyngeal swab on day 3, day 6 and day 9 during the 7 to 10-day course of antiviral treatment were collected from the patients and tested for sars-cov-2 nucleic acids by rt-pcr. sars-cov-2 clearance in covid-19 patients was defined as two consecutive negative-detection of sars-cov-2 rna in nasopharyngeal swab samples with an interval of over 24 hours. adverse events were monitored throughout the trial, reported and graded based on who toxicity grading scale for determining the severity. the peak levels of sars virus were around 10 days after onset and then the viral level j o u r n a l p r e -p r o o f began to decrease without effective antiviral treatment in sars patients (peiris et al., 2003) .considering the homology of gene sequences of sars-cov-2 and sars was over 90% (zhu et al., 2020) , we assumed that the intervention of antiviral drugs in covid-19 patients would likely enhance or shorten the time to viral clearance. in this regarding, the primary endpoint for this study was decided as the sars-cov-2 clearance rates in covid-19 patients assessed on day 6 of antiviral treatment. the secondary endpoint was median time to sars-cov-2 clearance. statistical analysis was performed on an intent-to-treat basis, and all patients randomized and treated at least once with the study medications were included for the primary analysis. for patient demographics information and baseline disease characteristics, qualitative variables were compared among treatment groups with the use of chi-square test, and quantitative variables were compared with the use of an anova model. only the overall differences among the three treatment groups were tested (based on null hypothesis, "all three groups were the same", against an alternative hypothesis, "at least one group was different")and therefore, no pairwise comparison was performed for baseline characteristics. for the primary endpoint, sars-cov-2 clearance rate, estimates of the rates were calculated based on a binomial distribution. difference between treatment groups was tested using the chi-square test. to control the overall significance level for the study, the three pairwise comparisons for the primary endpoint were performed at the two-sided alpha = 0.05 using a closed testing procedure according to the following order:① novaferon plus lopinavir/ritonavir vs. lopinavir/ritonavir alone; ② novaferon alone vs. lopinavir/ritonavir alone; ③ novaferon plus lopinavir/ritonavir vs. novaferon alone. for the secondary endpoint, time to sars-cov-2 clearance, median time for each group was j o u r n a l p r e -p r o o f estimated with the use of the kaplan-meier method and treatment differences were tested using log-rank test. all tests were two-sided, with a p value of less than 0.05 considered to indicate statistical significance. analysis was conducted using sas v9.2. for missing sars-cov-2 clearance status, last observation carried forward (locf) analysis was presented as the primary analysis. for purpose of sensitivity analyses, complete case analysis and worst case imputation methods were also performed. for the worst case imputation, missing sars-cov-2 status was replaced with 'positive'. the planned sample size of 90 patients (30 patients per group) was not determined based on statistical consideration. adverse events were reported and graded using who toxicity grading scale for determining the severity. incidence of adverse events was summarized descriptively without a formal statistical test. incubation of novaferon (0.1⁓100ng/ml) with sars-cov-2-infected vero e6 cells resulted in the dose-dependent reductions of the sars-cov-2 rna that was released from the infected vero e6 cells. the half-maximal effective concentration (ec50) of novaferon was 1.02 ng/ml. the tested novaferon concentrations showed minimal cytotoxicity to vero e6cells, and the half-maximal cytotoxic concentration (cc50) was over 100ng/ml. the selectivity index (cc50/ec50) was over 98. these data indicated that novaferon effectively inhibited the viral replication within sars-cov-2-infected cells. in addition, healthy vero e6 cells that were previously incubated with novaferon resisted the entry of sars-cov-2into cells, as indicated by the reduction of cellular viral rna after novaferon was removed and the treated cells were exposed to sars-cov-2 later. novaferon exhibited this preventive effect efficiently with the ec50(0.1 ng/ml) lower than the ec50 for inhibiting healthy cells to resist the viral attack. as presented in fig. 1 , a total of 92 patients with moderate or severe illness were assessed for the eligibility criteria and 3 patients were excluded. 89 patients were randomized into the study from february 1 to 20, 2020. of the 89 patients, 30, 30, and 29 patients were assigned into novaferon group, novaferon plus lopinavir/ritonavir group or lopinavir/ritonavir group respectively, among whom 84 were moderate illness and 5 severe illness. supported by the government policy of reimbursing covid-19-related expenses, patients were diagnosed, screened, and enrolled shortly after symptom onset. the median time (iqr) from symptom onset to antiviral drug administration were 4.0 days(3.0-6.5), 7.0 days(3.3-11.3), and 4.0days(3.0-6.0) in novaferon group, novaferon plus lopinavir/ritonavir group or lopinavir/ritonavir group respectively. enrollment screening excluded patients with co-existing serve cardiac, kidney or liver diseases as described in exclusion criteria, and none of the enrolled patients has been given steroids treatment. the baseline demographic and clinical characteristics of the 89 patients were summarized in table 1 .except some imbalances between the groups, there were no major differences between groups in demographic characteristics, baseline laboratory test results and disease severity at enrollment (table 1) . table 2summarized the complete rt-pcr test results of all 89 patients on day 3, day 6, and day 9 after starting drug administration. the negative results of sars-cov-2 nucleic acid detection in the tested samples served as the indicator of in vivo sars-cov-2 clearance in patients. the sars-cov-2 clearance rates on day 3, day 6, and day 9 in three treatment groups were presented and compared (table 2) .on day 3, sars-cov-2 clearance rates were 16.7%(5/30) in novaferon group, 36.7% (11/30) in novaferon plus lopinavir/ritonavir group, and 10.3% (3/29) in lopinavir/ritonavir group respectively. sars-cov-2 clearance rate in novaferon plus lopinavir/ritonavir group was significantly higher than in lopinavir/ritonavir group on day 3 (36.7%vs. 10.3%, p = 0.0175). no significant difference between novaferon group and novaferon plus lopinavir/ritonavir group was observed. on day 6, sars-cov-2 clearance rates in novaferon group and novaferon plus lopinavir/ritonavir group reached to 50.0% (15/30) and 60.0% (18/30) respectively, and were significantly higher than in lopinavir/ritonavir group (50.0% vs.24.1%, p = 0.0400, and 60.0% vs.24.1%, p = 0.0053, respectively). there was no statistically significant difference between novaferon group and novaferon plus lopinavir/ritonavir group, suggesting the similar extents of enhancedsars-cov-2 clearance on day 6 by novaferon alone or together with lopinavir/ritonavir. on day 9, sars-cov-2 clearance rates were 56.7% (17/30) in novaferon group, 70.0% (21/30) in novaferon plus lopinavir/ritonavir group, and 51.7% (15/29) in lopinavir/ritonavir group. there were no statistically significant differences between the groups. the median time to sars-cov-2 clearance were 6 days, 6 days, and 9 days for novaferon group, novaferon plus lopinavir/ritonavir group, and lopinavir/ritonavir group respectively, indicating a 3-day reduction of time to sars-cov-2 clearance in both novaferon and novaferon plus lopinavir/ritonavir groups comparing with lopinavir/ritonavir group (table 3) .during the observation period, none of the moderate ill patients in novaferon group and novaferon plus lopinavir/ritonavir group progressed j o u r n a l p r e -p r o o f to severe illness. in contrast, 4 moderate ill patients in lopinavir/ritonavir group progressed to severe illness. analyses based on both complete case analysis and worst case imputationforsars-cov-2 clearance rates showed little differences with the locf analysis, and the statistical conclusions for all the treatment comparisons remained the same. no severe adverse events (sae) associated with the tested antiviral drugs were reported. the observed adverse events (ae) were grade1, or grade 2, and summarized in table 4 . no specific aes were related to novaferon treatment, and certain reported adverse events overlapped with the disease symptoms and laboratory findings. the observed adverse reactions did not need extra medical interventions or cause termination of antiviral treatment. no matter whether exhibiting good, poor or none anti-covid-19 effects, lopinavir/ritonavir in this study served as the control and allowed us to assess the antiviral effects of novaferon by analyzing the differences between novaferon and lopinavir/ritonavir. in this regarding, the significantly highersars-cov-2 clearance rates on day 6 (the primary endpoint) inpatients with treatment of novaferon alone or together with lopinavir/ritonavir comparing with lopinavir/ritonavir alone indicated that j o u r n a l p r e -p r o o f novaferon indeed exhibited antiviral effectsincovid-19patients. the 3-day reduction of time to sars-cov-2 clearance in patients with novaferon treatment further supported the antiviral effects of novaferon. as viral shedding in the early stages of covid-19 represents a major challenge for controlling the transmission of sars-cov-2 (wölfel et al.,2020) , the effective viral clearance in patients undergoing novaferon treatment in the early course of disease was valuable in clinical setting. the negative detection of sars-cov-2 in samples from the respiratory system indicated the elimination of the viral shedding in patients. this in turn would contribute to the effective reduction of virus transmission by early stage patients who have been found to have the highest viral loads (pan et al.,2020) . the antiviral effects of novaferonincovid-19 patients were consistent with the laboratory findings. inhibition of the viral replication by novaferon at cellular level was very efficient as indicated by the low ec50(1.02 ng/ml). more interestingly, healthy cells that were pretreated by novaferon obtained the ability, in the absence of novaferon, to resist the viral entry into cells when the treated cells were exposed to sars-cov-2 later (ec50 0.1 ng/ml). it might be worth to explore the potential use of novaferon as a preventive agent for high risk population, especially for health care workers who have to routinely contact covid-19 patients. the viral loads in covid-19 patients were reported to reach peak levels around 5⁓6 days after symptom onset (pan etal.,2020) , and for severe patients，the average time from the onset of symptoms to severe illness took about one week(who,2020).the early clearance of sars-cov-2 might help to shorten the disease course or to prevent the disease progress in patients with mile to moderatecovid-19. considering the high viral loads and peak levels of sars-cov-2were found in first week of symptom onset, the increased sars-cov-2 clearance rates on day 6 in covid-19 patients with novaferon treatment were j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f a trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 role of lopinavir/ritonavir in the treatment of sars: initial virological and clinical findings first case of 2019 novel coronavirus in the united states genomic characterization, and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding therapeutic options for the 2019 novel coronavirus (2019-ncov) novaferon, a novel recombinant protein produced by dna-shuffling of ifn-alpha, shows antitumor effect in vitro and in vivo viral load of sars-cov-2 in clinical samples clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study a new coronavirus associated with human respiratory disease in china world health organization potential interventions for novel coronavirus in china: a systematic review a pneumonia outbreak associated with a new coronavirus of probable bat origin a novel coronavirus from patients with pneumonia in china recombinant human interferon-like proteins(patent no. us 7,625,555 b2) the impacts of baseline clinical characteristics and hepatitis b virus mutations on curative effects chronic hepatitis b treatment with novaferon report of the who-china joint mission on coronavirus disease virologic assessment of hospitalized patients with covid-2019 lpv/r*+novaferon n=30, n(%) lpv/r n=29, n(%) we thank all the medical and management staff, who came from hospitals across changsha city and worked at the first hospital of changsha, for their courage and dedication to covid-19 patient care and overall operations of the hospital during the difficulty time. key: cord-306200-d5qn65k0 authors: petersen, eskild; mccloskey, brian; hui, david s; kock, richard; ntoumi, francine; memish, ziad a; kapata, nathan; azhar, esam i; pollack, marjorie; madoff, larry c.; hamer, davidson h; nachega, jean b; pshenichnaya, n.; zumla, alimuddin title: covid-19 travel restrictions and the international health regulations – call for an open debate on easing of travel restrictions date: 2020-04-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.029 sha: doc_id: 306200 cord_uid: d5qn65k0 nan correspondence: eskild petersen: email: eskild.petersen@gmail.com the covid-19 pandemic caused by the novel coronavirus (sars-cov-2) has caused national governments worldwide to mandate several generic infection control measures such as physical distancing, self-isolation, and closure of non-essential shops, restaurants schools, among others. some models suggest physical distancing would have to persist for 3 months to mitigate the peak effects on health systems and could be required on an intermittent basis for 12 to 18 months [flaxman s et al. 2020 ]. apart from these control measures travel restrictions during the early phase of the china outbreak were useful to confine it to wuhan, the major source of the outbreak [kraeamer et al, 2020] although ultimately these measures did not prevent the spread of covid-19 to other regions of china. the global spread of the sars-cov-2 has clearly been associated with regional and international travel which has contributed to the pandemic [candido et al. 2020 ]. to limit cross-border spread, both regionally and globally, many countries have swiftly adopted sweeping measures, including full lockdowns of shops, companies, shutting down airports, imposing travel restrictions and completely sealing their borders, to contain transmission [gostin lo et al 2020] . the grounding of international travel as part of the global response to prevent spread has caused profound disruption of travel and trade and has threatened the survival of many airlines, travel companies, and associated businesses. travel bans to affected areas or denial of entry to passengers coming from affected areas are usually not effective in preventing the importation of cases but have a significant economic and social impact. since the who declaration of a public health emergency of international concern on 30 january 2020, and as of 8 th april, 2020, 180 countries have reported to who additional health measures that significantly interfere with international traffic in relation to travel to and from china or other countries, ranging from denial of entry of passengers, visa restrictions or quarantine for returning travellers [who 2020a ]. to re-start the world economy again it will be important to ease travel restrictions as soon as possible. whilst travel restriction measures that significantly interfere with international traffic may be justified at the beginning of an outbreak, since they allow countries time to implement effective preparedness measures based on careful risk assessment, they should be based on a reasoned scientific evaluation of the available evidence on their possible effectiveness. they should also be time-limited and reconsidered and revisited on a regular basis as better information on both the effectiveness and the socio-economic impact of the measures emerges. thus an open debate is now required on when and how they need to be lifted. this debate could usefully be framed in the context of the international health regulations. the purpose of the who international health regulations [who, 2020b] is to 'prevent, protect against, control and provide a public health response to the international spread of disease in ways that are commensurate with and restricted to public health risks, and which the who's advice, based on many years of international outbreak response, was considered by many to be reasonable and evidence-based but the recommendation on travel restrictions has not been heeded by governments and politicians in the face of rapid spread of covid-19 between countries. this highlights the apparent dissonance between scientific advice and political realities [and indeed public perception]. as many countries are now approaching the peak or flattening phase of the epidemic curve this dissonance will again become forefront and an open debate is required on lifting of travel restrictions. several questions need to be considered: why have several countries systematically ignored who's advice on not restricting travel during the covid-19 outbreak? is it that the advice was considered wrong or that the advice was inconsistent with the public perception that closing borders was a "sensible" thing to do? 2. given that countries have unilaterally made decisions to close down international travel, how can we get better science and evidence into decisions about lifting these restrictions as the outbreak resolves so that international trade and the global economy can start to recover? it seems inevitable that countries will move at different speeds to these decisions, reflecting the different evolution of the outbreak in each country. promoting a risk-based approach to lifting the travel restrictions that might vary from country to country could provide a way forward but it will need a degree of international coordination to avoid a random, possibly chaotic, certainly confusing, and probably ineffective process. this coordination should come from who in line with the mandate given to who by the member states through the ihr. countries with still very few cases and potential to arrest and eliminate the few cases that they have, should not open up travel without very strict quarantine for arrivals. this could reduce the conflict between science-based advice and political decision making. what mitigating measures will be available to reduce the risk of a resurgence of the outbreak as public health measures, including travel restrictions, are eased? in particular what role (if any) will pcr and immunity (serology) testing play in managing the impact of lifting restrictions? it will be imperative that countries easing restrictions (whether social or physical distancing or travel restrictions) have in place resources and capacity for detecting, testing and quarantining all new cases arising as well as tracing and tracking all contacts. there has been evidence of global capacity issues with pcr tests and possibly of market influencing to secure testing capacity in some countries. should there be, within the spirit of the recent g20 statement [g20, 2020], international cooperation facilitated by who to ensure testing capacity is made available in a managed way to countries as and when they need it most? indeed, the who the 7 th april certified the first two pcr tests [who, 2020c] and advice on the use of point-of-care tests [who, 2020d] the majority of persons who have been infected sars-cov-2 recover and appear to be immune and non-infectious [to kk-w et al. 2020 ] although recurrence have been reported but need further confirmation [zhou l et al. 2020 ]. we do not know for how long such j o u r n a l p r e -p r o o f 5 immunity lasts but neutralizing antibodies was found more than two years after infection with sars-cov [wu lp et al. 2007] . a validated, specific and sensitive test to detect sars-cov-2specific-igg is urgently required to support countries' efforts to control the outbreak. there is currently no evidence to recommend serology as an immunity passport and we do not have any long-term data about how effective and long-lasting immunity might be but there will undoubtedly be pressure to implement such measures. it would be helpful if this was coordinated to ensure a consistent approach globally, with consistent standards and requirements, and such an approach is also clearly within who's ihr mandate. as sars-cov-2 continues to spread across different geographical regions, with different epidemiological patterns being seen, we await how it will evolve over time and across seasons [in both the north and south hemisphere]. meanwhile ongoing proactive surveillance should be maintained and the search for effective serological tests, treatments and vaccines be pursued vigorously. as we start to emerge from the initial phase of the outbreak, international cooperation, collaboration, leadership and authority will be critical -where will it come from? author declarations: all authors have a specialist interest in emerging and re-emerging pathogens and report no potential conflicts. routes for covid-19 importation in brazil estimating the number of infections and the impact of non-pharmaceutical interventions on covid-19 in 11 european countries. imperial college, london g20 leaders' statement: extraordinary g20 leaders' summit statement on governmental public health powers during the covid-19 pandemic: stay-at-home orders, business closures, and travel restrictions the effect of human mobility and control measures on the covid-19 epidemic in china temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study advice on the use of point-of-care immunodiagnostic tests for covid-19 geneva 8 th duration of antibody responses after severe acute respiratory syndrome cause analysis and treatment strategies of "recurrence" with novel coronavirus pneumonia [covid-19] patients after discharge from hospital key: cord-338225-8dlxnpcn authors: de meyer, sandra; bojkova, denisa; cinatl, jindrich; van damme, ellen; meng, christophe buyck; van loock, marnix; woodfall, brian; ciesek, sandra title: lack of antiviral activity of darunavir against sars-cov-2 date: 2020-05-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.085 sha: doc_id: 338225 cord_uid: 8dlxnpcn abstract objectives given the high need and the absence of specific antivirals for treatment of covid-19 (the disease caused by severe acute respiratory syndrome-associated coronavirus-2 [sars-cov-2]), human immunodeficiency virus (hiv) protease inhibitors are being considered as therapeutic alternatives. methods prezcobix/rezolsta is a fixed-dose combination of 800mg of the hiv protease inhibitor darunavir (drv) and 150mg cobicistat, a cyp3a4 inhibitor, which is indicated in combination with other antiretroviral agents for the treatment of hiv infection. there are currently no definitive data on the safety and efficacy of drv/cobicistat for treatment of covid-19. the in vitro antiviral activity of darunavir against a clinical isolate from a patient infected with sars-cov-2 was assessed. results drv showed no activity against sars-cov-2 at clinically relevant concentrations (ec50 >100μm). remdesivir, used as a positive control, showed potent antiviral activity (ec50 =0.38μm). conclusions overall, the data do not support the use of drv for treatment of covid-19. overall, the data do not support use of darunavir for treatment of covid-19 cov-2]), human immunodeficiency virus (hiv) protease inhibitors are being considered as 23 therapeutic alternatives. the virus was subsequently identified as a coronavirus (cov), in addition to sars-cov-1 and 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 visual cpe read-out ec50 > 100 μm; mtt ec50 > 100 μm; cc50 >100 μm covid-19 -the search for effective therapy cobicistat-boosted darunavir in hiv-1-infected adults: week 48 results of a phase iiib, open-276 label single-arm trial remdesivir and chloroquine effectively 278 inhibit the recently emerged novel coronavirus (2019-ncov) in vitro analysis of therapeutic targets for key: cord-309032-idjdzs97 authors: zhou, feng; you, chong; zhang, xiaoyu; qian, kaihuan; hou, yan; gao, yanhui; zhou, xiao-hua title: epidemiological characteristics and factors associated with critical time intervals of covid-19 in eighteen provinces, china: a retrospective study date: 2020-10-09 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1487 sha: doc_id: 309032 cord_uid: idjdzs97 background as covid-19 ravages continuously around the world, more information on the epidemiological characteristics and factors associated with time interval between critical events is needed to contain the pandemic and to assess the effectiveness of interventions. methods individual information on confirmed cases from january 21 to march 2 was collected from provincial or municipal health commissions. we identified the difference between imported and local cases in the epidemiological characteristics. two models were established to estimate the factors associated with time interval from symptom onset to hospitalization (toh) and length of hospital stay (los) respectively. results among 7,042 cases, 3392 (48.17%) were local cases and 3304 (46.92%) were imported cases. since the first intervention was adopted in hubei on january 23, the daily reported imported cases reached a peak on january 28 and gradually decreased since then. imported cases were on average younger (41 vs. 48), and had more male (58.66% vs. 47.53%) compared to local cases. furthermore, imported cases had more contacts with other confirmed cases (2.80 ± 2.33 vs. 2.17 ± 2.10), which were mainly within family members (2.26 ± 2.18 vs. 1.57 ± 2.06). the toh and los were 2.67 ± 3.69 and 18.96 ± 7.63 days respectively, and a longer toh was observed in elderly living in the provincial capital cities that were higher migration intensity with hubei. conclusions measures to restrict traffic can effectively reduce imported spread. however, household transmission is still not controlled, particularly for the infection of imported cases to elderly women. it is still essential to surveil and educate patients about the early admission or isolation. as of september 20, 2020, a total of more than 30 million confirmed cases of coronavirus disease 2019 , as well as more than 900,000 deaths had been reported by world health organization (who) in the worldwide (organization, 2020a) . at the same time, china had reported 85,291 lab confirmed cases with 4,634 deaths (china national health commission of the people's republic of, 2020a). despite the who and international community declared and took many efforts to control this pandemic in time, our knowledge about the covid-19 is still very limited, and the number of daily reported cases is still increasing sharply worldwide (organization, 2020b) . in the context of the rapid spread of covid-19, a full understanding of the epidemiological characteristics of this infectious disease is crucial in epidemic control and public policy practices. several studies conducted in china, italy and the united states have reported some epidemiological characteristics of covid-19 in the initial phase (grasselli et al., 2020 , liang et al., 2020 , price-haywood et al., 2020 , richardson et al., 2020 , wu and mcgoogan, 2020 , however, there is still a lack of research on the space-time characteristics in the populations of imported and local cases respectively which is of great significance. imported cases play a very important role in the disease spreading, especially it is an indicator for predicting new clusters of infections. understanding its epidemiological characteristics would help us to assess the possible effect of non-pharmaceutical interventions (npis), such as travel restrictions (desjardins et al., 2020 , gilbert et al., 2020 . furthermore, considering the changes in susceptible populations, exposure opportunity and intervention of disease over epidemic progresses and locations, the epidemiological characteristics of disease should hence be estimated spatiotemporally in order to better describe the epidemic (zhang j. et al., 2020) . for example, the space-time characteristics of covid-19 revealed by previous studies can prioritize locations and the best time for different npis (desjardins et al., 2020 , lai s. et al., 2020 , masrur et al., 2020 . therefore, exploring the epidemiological characteristics of j o u r n a l p r e -p r o o f imported cases from a space-time perspective is critical and provides guidance for countries on interventions taken at different periods and regions, specifically in resource-scarce countries and regions. as a highly contagious disease, early detection, isolation, hospitalization and diagnosis of covid-19 are also important for control and they can effectively reduce the risk of disease transmission (bi et al., 2020 , rong et al., 2020 , thompson, 2020 . delay in hospitalization or isolation may lead to prolonged periods of infectiousness, and increase the difficulty and burden of infectious disease control. previous studies have described some characteristics of patients with covid-19 including the time interval between key events (liang et al., 2020 , tian et al., 2020 . in addition, existing literature also brought to light the reduction in the time interval from symptom onset to hospitalization/isolation after various interventions , zhang j. et al., 2020 . however, little is known about individual-level influence factors associated with delaying hospital admission and length of hospital stay. identifying these factors would not only help us predict the medical burden and reasonably allocate medical resources, but also would inform response efforts across the world. in this study, we described the spatiotemporal distribution of the covid-19 in eighteen provinces of china (outside hubei province) and investigated the epidemiological characteristics in the population of imported cases and local cases, from the beginning of this epidemic until it was under good control. we further assessed the critical influence factors associated with time interval from symptom onset to hospitalization (toh) and length of hospital stay (los), including demographic and temporal and spatial characteristics. j o u r n a l p r e -p r o o f we constructed a retrospective cohort study for covid-19 confirmed cases, based on the detailed information published by the provincial or municipal health commissions in eighteen provinces of china (outside hubei province) from january 21 to march 2. the details of sampling and data collection are shown in figure 1 . data collectors were trained and divided into five groups of two according to provinces to collect timely epidemiological data of confirmed cases. linkmed edc were used for data entry, the two collectors in each group entered the same data, and we conducted data verification and consistency test in real-time. specifically, demographic characteristics, epidemiological history and date of critical event were extracted from the official report of the confirmed case details. (1) demographic information including age, gender, residence at the time of diagnosis and type of symptoms were included in our analysis. (2) epidemiological history includes history of travel or residence in other regions and contact history of confirmed cases. according to whether the patient had a travel or residence history in other regions within 14 days before diagnosis and likely exposure to pathogens in that regions, the patient was divided into imported and local cases. similarly, we can identify whether patients had contacted with confirmed cases of family and non-family members. (3) the dates of events include the date of symptoms onset, hospitalization/isolation, cdc diagnosis and recovery/death. hospitalization/isolation is defined as a patient receiving regular hospital treatment (not includes small medical institutions such as clinics and community health service centers), or a mandatory isolation measure implemented by the community. in this study, we used the time interval between two events to analyze this data, including time interval from symptom onset to hospitalization (toh) and length of hospital stay (los). additionally, we also collected information on the intensity of migration from hubei to these 18 provinces in the week before january 23, which was obtained from the baidu j o u r n a l p r e -p r o o f migration map (baidu, 2020) . migration intensity between provinces and hubei was categorized into four levels: strong connection (≥0.15%), medium connection [0.05%-0.15%), weak connection [0.03-0.05%) and very weak connection (<0.03). finally, according to the daily trend of new cases and date of intervention, we divided the entire epidemic into five periods from the beginning of the epidemic (jan 21) to mar 2. the first period is before january 23, when wuhan took measures of traffic restrictions and lockdown, since then every week works as one period, until the last period is a recession of this epidemic after february 14. we described the epidemic scale in 18 provinces and the proportion of imported cases spatiotemporally. meantime, the demographic characteristics of imported and local cases were reported. in addition, two models were established to identify and quantify the relevant sociodemographic factors to toh and los respectively. in the first model, we estimated the factors associated with toh using a generalized linear model with a poisson distribution and a log link. besides, the odds ratio (or) and their 95% confidence intervals (ci) were calculated after incorporating multiple variables (coxe et al., 2009 , sas, 2016 . in the second model, an accelerated failure time (aft) model was used to handle the survival data with both left and right censored (kalbfleisch, 2002 , paul, 2010 . in our study of analyzing factors associated with los, left censoring would occur if we know that a patient recovered before marth 2, but the exact time cannot be obtained. similarly, right censoring would occur for patients who are confirmed in the later phase of the epidemic. moreover, we included the toh in the model and used the hazard ratio (hr) and their 95% cis to identify the difference in los among recovered patients with different characteristics. based on the distribution of los which is denoted by t, we established the weibull model, written as, where ε is a random disturbance term, and β 0 ,...,β , and σ are parameters to be estimated. then we applied a likelihood function with censored to estimate the parameter values. inc., north carolina, usa). p<0.05 was considered statistically significant. among 7,042 cases, 3392 (48.17%) of patients were local cases and 3304 (46.92%) of patients were imported cases, and less than 5% (346) of other patients were unable to confirm their travel history within 14 days before diagnosis. the temporal and spatial distribution of imported and local cases is shown in figure 2 . from panel a, we can see that the greater the intensity of migration with hubei, the more cases in the province. for provinces with migration intensity greater than 0.03%, the proportion of imported cases to total cases was about 50%. however, for provinces including tianjin, ningxia and hebei with very weak connection (<0.03%) with hubei, they had more local cases than imported cases. since the first intervention was adopted in hubei on january 23, the daily reported imported cases reached the highest on january 28, and the proportion of imported cases to the total cases gradually decreased over time, reaching 50% on february 2 ( figure 2b ). j o u r n a l p r e -p r o o f 44.13%). for time interval, the frequency and best-fitting probability density function for toh and los are present in figure 3 respectively. as shown in the top half of the left panel of table 3 shows the results of the first model for the influence factors of toh. a longer toh was observed in older and provincial capital cases. the older the case is , the longer the toh. as compared with the cases younger than 20, especially for cases older than furthermore, patients who lived in regions with lower migration intensity with hubei province had shorter toh. particularly, as for patients living in regions where had the migration intensity more than 0.15%, migration intensity (1) between 0.05% and 0.15%, had down to 0.87 times decreased risk of longer time, (2) between 0.03% and 0.05%, had down to 0.74 times, (3) less than 0.03%, had down to 0.69 times. in addition, there is no significant differences in toh between imported and local cases. the right panel of table 3 gives the hr estimates of related factors associated with los. there were no significant differences in los among different gender or age groups. it also showed that differences in los relative to city type and fever symptoms were not statistically significant. while, patients clearly contacted with family-confirmed case had a longer los (hr=1.05; 95% ci: 1.01,1.09) than patients who did not clearly contact. moreover, we found j o u r n a l p r e -p r o o f that local patients had a shorter hospital stay than imported cases (hr=0.95; 95% ci: 0.91,0.99). furthermore, patients reported in the later periods of this epidemic had a shorter hospital stay than patients in the initial epidemic (hr=0.66; 95% ci: 0.57,0.77). compared with patients whose toh was less than or equal to one day, los of patients whose toh was more than 4 days was reduced by 0.05 percentage. and the similar result appeared in patients whose toh was 2-3 days (hr=0.94; 95% ci: 0.89,0.99). comprehensive epidemiological characteristics of the covid-19 covering the entire periods of epidemic and summaries of the experience from china are useful in public health control. in this study, we described the epidemiological characteristics of imported and local cases, including temporal and spatial characteristics. indeed, regions with greater migration intensity with hubei had more imported cases. after the lockdown measures taken by cities in hubei since january 23 towards the interruption of sustained covid-19 transmission outside hubei province (nie et al., 2020) . we found the daily reported imported cases reached a peak on january 28 and gradually decreased since then. these suggest that traffic restrictions or lockdown in the epicenter can effectively reduce the export of cases (islam et al., 2020 , zhang j. et al., 2020 . moreover, outside of the epicenter, it is also obvious that timely restriction and quarantine of suspicious imported individuals with a travel history of epicenter can effectively reduce the transmission by imported cases in local , kwok et al., 2020 , lai c. k. c. et al., 2020 . even in the provinces that were not in close contact with hubei, the surveillance of imported cases could not still be overlooked. taking tianjin, ningxia and hebei province as examples, local cases were twice as large as imported cases, which was related to the several local gathering events of imported cases , dong et al., 2020 , zhang s. x. et al., 2020 . this study confirms previously described characteristics (liang et al., 2020, wu and mcgoogan, 2020) , but also highlights the difference between imported and local cases. throughout this epidemic, imported patients focused on younger, had a higher proportion of male and had more provincial capital residents compared to local cases. this may match the situation that labor exports are mainly the young and middle-aged male in china. this result also insinuates older women living in non-provincial capital cities were at greater risk of exposure when the epidemic spreads to the local. a study on household transmission also founded similar results (xu et al., 2020) . moreover, the proportion of clearly confirmed case contact history in local cases was higher than that in imported cases. this may be due to the complicated epidemic chain in hubei province in the initial phase of the epidemic, which made it difficult to track the contact history of imported cases. nonetheless, approximately 40% of local cases may be attributed to the household transmission. among the patients who were clearly exposed to confirmed cases, imported cases had more contacts with other confirmed cases than local cases on average, and contacts were mainly family members. although we are unable to determine the infectious relationship between them, it might partly explain household transmission caused by imported cases was more prominent. this suggests that after npis such as restricting population movement were taken. more effective interventions were still needed to be taken to control household transmission simultaneously, especially for the infection of imported cases to elderly woman in non-provincial capital cities. indeed, the chinese government encouraged people to stay at home as much as possible (lai s. et al., 2020) . while, the cases that have migrated out from hubei before january 23 still have the risk of household transmission in local. therefore, emergency measures were taken by local governments across china to strengthen the tracking and isolation of recent travelers from hubei (china national health commission of the people's republic of, 2020b, china the state council of the people's republic of, 2020), which reduced this risk to a certain extent. moreover, our study showed that the daily local cases reached a peak on the 14th day (february 6) after the lockdown, and then gradually declined. this also illustrates the early response of the government is very important for containing the local spread of imported cases. our findings show that there was a lag of 2.67 days from symptom onset to hospital admission, and the average length of hospital stay was about 19 days, which were similar to previous studies conducted in china (khalili et al., 2020 , liang et al., 2020 , linton et al., 2020 . surprisingly, we found that the older the patients are, the longer the hospitalization delays. considering the situation that medical resources outside hubei province had not reached saturation, this might be related to the hospital admission pattern of viral respiratory diseases or the lack of recognition of the disease in elderly patients (petrilli et al., 2020) . besides, the toh at the later phase of the epidemic showed a rebound trend. cases reported in the later phase of the epidemic had a slack attitude in seeking medical resources and the decline in control efforts were possible reasons. however, research in china (outside hubei province) during january 21 to february 17 demonstrated a shorter hospital admission delay from january 28 to february 17 (4.4 vs. 2.6 days) (zhang j. et al., 2020) . before adjusting for other factors, our research also showed a slightly shorter hospital admission delays in the week after january 23. except for the different study population and period, we consider this result may be affected by the confounder. our research included the later phase of the epidemic and adjusted other demographic factors. this study also confirms that patients living in provincial capital that closely connected to the epicenter had a longer toh. this provides new demands on the epidemic prevention and control, that is, in provincial capital cities close to the epicenter, case tracking, surveillance and education of immediate admission/isolation should be emphasized. a mathematical model study showed that if the mean time from symptom onset to hospitalization can be halved by surveillance, then the probability that a case leads to transmission is very low (thompson, 2020) . interestingly, we found associations of clear republic of, 2020b). in addition, our results also found that the average los of 19 days will not decrease by early admission. perhaps it is related to the characteristics of the viral infectious disease. by contrast, the decrease in los in the later phase of the epidemic may be due to the continuous improvement of medical technology for this disease. this study included a large study cases during an entire epidemic and used a novel methodology. however, there are some limitations. first, as a retrospective study, since the date of symptom onset is self-reported based, there may be recall bias. second, although we made an effort to collect patient discharge information, we still could not obtain the discharge data of some patients. fortunately, nearly 90% of patients were discharged from the hospital at the end-point of observation on march 2, which provides an opportunity for the statistical methodology using survival data with left censoring. third, given the proportion of death cases in the study population was particularly small, which is less than 1%, the impact of death truncation was not considered when analyzing the length of hospitalization. finally, our study did not include the southeast provinces, but henan and zhejiang province were similar to those provinces in intensity of migration and scale of epidemic, and our results are also consistent with several studies conducted in shenzhen and hong kong in epidemiological characteristics during the same period (bi et al., 2020 , lai c. k. c. et al., 2020 . in patients' education about early admission or isolation should still be attached great importance in the future prevention and control, especially for the elderly living in provincial capital cities that were more closely connected with the epicenter. feng zhou: data collection, data analysis, writing. chong you: data collection, writing. xiaoyu zhang: data analysis. kaihuan qian: data collection. yan hou: data collection. yanhui gao: data analysis. xiao-hua zhou: study design. not required. the study was anonymous, and individual information was collected from provincial or municipal health commissions, which is a public data to help control this epidemic. no potential conflict of interest exits in the submission of this manuscript, and manuscript is approved by all authors for publication. panel a shows the frequency (blue histograms) and best-fitting probability density function (poisson, red curves) for time interval from symptom onset to hospitalization(≥0). panel b shows the frequency (blue histograms) and best-fitting probability density function (weibull, red curves) for length of hospital stay. j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f baidu migration map epidemiology and transmission of covid-19 in 391 cases and 1286 of their close contacts in shenzhen, china: a retrospective cohort study 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sas/stat 14.2 user's guide: the glimmix procedure (chapter novel coronavirus outbreak in wuhan, china, 2020: intense surveillance is vital for preventing sustained transmission in new locations characteristics of covid-19 infection in beijing characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the chinese center for disease control and prevention household transmissions of sars-cov-2 in the time of unprecedented travel lockdown in china epidemiological and clinical characteristics of 333 confirmed cases with coronavirus disease evolving epidemiology of novel coronavirus diseases 2019 and possible interruption of local transmission outside hubei province in china: a descriptive and modeling study the analysis of clinical characteristics of 34 novel coronavirus pneumonia cases in ningxia hui autonomous region symptoms fever # gender male 2430 2.84(3.53) 2(0-4) reference 654 19 non-family-confirmed patient contact history # unclear 3962 2.87(3.55) 2(0-5) reference we thank xueqing liu, yuying li j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f key: cord-293630-zc8huo1j authors: capone, alessandro title: simultaneous circulation of covid-19 and flu in italy: potential combined effects on the risk of death? date: 2020-08-05 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.077 sha: doc_id: 293630 cord_uid: zc8huo1j based on data updated to may 20, 2020, in italy the total recorded number of patients who died due to covid-19-related reasons is 31,851. demographic and clinical characteristics of died patients (including the number of comorbidities) are extremely relevant, especially to define those with a higher risk of mortality. health authority recommends flu vaccination in a number of categories at risk of serious medical complications: subjects over 65, patients with diabetes, cardiovascular diseases, copd, renal failure, cancer, immunodeficiencies, chronic hepatopathies and chronic inflammatory bowel diseases. the peak of the seasonal flu certainly preceded the pandemic one; however, it would seem clear that for a while the two viruses have been circulating simultaneously in italy. hence, after its peak, influenza-like illness-related (ili) deaths started to grow again. while some of the excess mortality reported in the ili group may be attributable to covid-19, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? a cooperation mechanism intended at establishing an absolute advantage over the host could also be assumed. this system often takes place to boost their reproductive probabilities. a characterization of patients died due to virus-related reasons can be done by cross-linking data stored in different warehouses of the same geographical area and developing electronic health records. it would be of great relevance to identify patients at a very high risk of mortality as a result of an overlapping or combination of risk factors reported separately in patients died from covid-19 or influenza. the description of the subgroup of patients at higher risk of mortality will be crucial for the prioritization and implementation of future public health prevention and treatment programmes. social distancing and other forms of precautionary public health measures have led to an effective control of beta coronavirus circulation in china, in italy, in other european countries, and in the usa as well. the blood toll paid in italy has been early and particularly high. at present, a "ceasefire" has been successfully achieved, but the war against covid-19 may not yet be over. indeed, a resurgence of infections due to beta coronavirus could be observed at the time of possible simultaneous circulation of covid-19 and influenza. such an event could be expected between late autumn and early winter this year. based on data updated to may 20, 2020, in italy the total recorded number of patients who came into contact with covid-19 and died corresponds to 31,851 [1] . preliminary case-fatality rate (cfr) among patients with covid-19 was estimated by onder et al [2] . the authors calculated the overall crude cfr corresponded to 7,2%, a remarkably higher value than the average reported in china (2,3%) [3] . demographic and clinical characteristics of died patients (including the number of comorbidities) are extremely relevant, especially to define those with a higher risk of mortality. age was recognised as one of the main risk factors for death associated with covid-19. the median age of deceased patients corresponded to 82 years (interquartile range: 74-88). this value is actually 20 years higher compared with the median age of infected patients (died patients 82 years, and infected patients 62 years, respectively) [4] . indeed, italy is one of the countries with the highest mean age in j o u r n a l p r e -p r o o f the world, along with japan and germany. pre-existing chronic diseases (diagnosed before the covid-19 infection) is an additional and substantial risk factor. the most frequent comorbidities reported include high blood pressure (67,9%), type 2 diabetes (30,0%), ischemic heart disease (28,2%) and renal failure (20,4%) [4] . unfortunately, the comorbidity assessment was derived from a carefully analysis of medical records of only 3,602 out of 33,532 died patients (about 10% of the overall supposed number) [4] . the average number of diseases observed in this population was 3,3 ± 1,9. on the other hand, a study lately performed by the italian national institute of health (iss), has shown that the excess of mortality associated with influenza-like illness (ili) was between 11,6 and 41,2 per 100,000, reaching a total of over 68,000 deaths in a 4-year time period [5] . in other words, patients with diabetes or other metabolic diseases (including those with a bmi >30), cardiovascular diseases, copd, renal failure, cancer, immunodeficiencies, chronic hepatopathies and chronic inflammatory bowel diseases [6] . the comparison between individuals at risk of mortality associated with both diseases (i.e. covid-19 and influenza) is of the utmost importance. indeed, a sub-stratification of patients at a very high risk of mortality might be predictable, in particular when the circulation of both viruses is supposed to occur in the same period. although attempts are being made to develop unique data collection platforms in italy, the information needed for accurate mortality risk estimation are commonly located in different repositories. this is true for both flu and covid-19. the national sentinel influenza surveillance system (known as influnet) is a network of general practitioners and pediatricians working as sensors and providing health care to at least 2% of the whole italian population [5] . as a consequence, estimating the role of flu in the overall mortality calculation is quite complex, since the diagnosis is not always confirmed by laboratory tests and most death cases are due to complications. for these reasons, although the death case is flu-related, flu may not be officially reported in all death certificates or registries. an indirect measure of its impact on mortality is given by the attributable excess of mortality, which can be calculated as the differential between the number of deaths observed during the flu season and the expected baseline value (in the absence of flu). several statistical regression models have been adopted to estimate the excess mortality attributable to influenza, considering the potential confounding effect of variables such as temperature, viral genotypes and age distribution patterns of the population [5, [7] [8] [9] . as far as covid-19 related deaths are concerned, the national institute of health (iss) has set up a specific web platform (similar to influnet) for epidemiological and immunological data collection, including recommended procedures for molecular diagnostics. however, as not all covid-19related death are assumed to have been hospitalized (i.e. some deaths occurred at home or often in health care homes), mortality data are supposed to be underestimated. nonetheless, it is very important to point out that the cause of death may not be surely or purely virus-dependent. this circumstance might be more frequently detected in patients with multiple comorbidities (more than 80% of died patients were affected by ≥ 2 comorbidities) [1] . moreover, data pertaining to drugs previously prescribed in patients with chronic clinical conditions (such as high blood pressure, diabetes, ischemic heart disease or copd) may not be detailed enough to identify patients at higher risk of death or those having factors increasing the risk itself. when we look at the shape and trend of curves over time, something immediately jumps out: the two death curves show an absolutely overlapping profile, although the magnitude of numbers associated with covid-19 is remarkably greater. that's not surprising. in any case, ili-related deaths have also started growing again. the peak of the seasonal flu has certainly preceded the pandemic one, however, it would seem clear that for a while the two viruses have been circulating simultaneously in italy. while some of the excess mortality reported in the ili group (in over 65) may be attributable to covid-19 infection actually, a question arises: do we have to consider this observation as a result of a random sequence of events or a potential relationship between the two viruses play a role? although they show a different binding affinity for their own specific redundant receptors (i.e. sialic acids of glycoproteins or glycolipids and ace2 for influenza and covid-19, respectively) [12, 13] , a cellular access pattern with different effectiveness, and consequently a diverse pathophysiology, both have an elective tropism for the respiratory tract. taking viral signaling into consideration, a j o u r n a l p r e -p r o o f cooperation mechanism intended at establishing an absolute advantage over the host could also be envisaged [14] . this system often takes place between different viral strains sharing the same interest in boosting their own reproductive probabilities. an example of effective viral cooperation was found in several oncogenic genotypes of high-risk and low-risk human papillomavirus [15] . moreover, the virulence also has usually turned out to be based on a cooperative effect between different genes which encoding for specific viral capabilities such as transmissibility and fatality [16] . hence, it's become increasingly clear that many viruses actively work together, teaming up to co-infect hosts and neutralise antiviral immune procedures. although at this stage it is merely a hypothesis that needs further investigation, the simultaneous or sequential infection of both viruses (covid-19 and influenza) leading to strengthen the effectiveness of the single infection cannot be excluded. at present, several data needed to estimate the real impact of influenza and coronavirus on overall mortality are still missing. in addition, assuming the potential simultaneous circulation of the two viruses (during the flu season), it is suggested that health authorities undertake a study (or perform a full assessment) specifically aimed at establishing the predominant risk factors of virus-related death. in particular, it would be of great relevance to identify patients at a very high risk of mortality as a result of an overlapping or combination of risk factors reported separately in patients died from covid-19 or influenza. subjects aged 65-70 years and over, suffering from hypertension or diabetes and especially those with metabolic syndrome or with 2-3 comorbidities (mentioned above in the two groups separately) are likely to be the elective target of prevention programmes. this is the reason why a similar investigation is mandatory. a detailed characterization of patients died due to virus-related reasons can be done by cross-linking data stored in different archives or warehouses of the same geographical area (classically a region). this guarantees a high intrinsic quality of the analysis and at the same time reduces the need to use j o u r n a l p r e -p r o o f alternative proxies or sources that could introduce a systematic bias. administrative and demographic databases can be queried retrospectively using a unique code referring to a single individual in order to develop a longitudinal electronic health record with a predetermined time interval. the description of the subgroup of patients at higher risk of mortality will be crucial for the prioritization and implementation of future public health prevention and treatment programmes such as a mass flu vaccination campaign. italy was not as ready to manage a so-rapid and dramatic pandemic, as many other countries were, actually. the gathering of data and assessment of consequences associated with covid-19 infections in italy took some time and appropriate responses (i.e. quarantine and social distancing measures) could have been delayed a bit. this event may also have contributed to smoothing the viral transmission and worsening some patients' clinical conditions. now, probably nothing will happen in the late fall, but an integrated pandemic plan for italy we must be prepared as soon as possible. ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. ☐the authors declare the following financial interests/personal relationships which may be considered as potential competing interests: characteristics of sars-cov-2 patients dying in italy case-fatality rate and characteristics of patients dying in relation to covid-19 in italy characteristics of and important lessons from the coronavirus disease national institute of health (istituto superiore di sanità) investigating the impact of influenza on excess mortality in all ages in italy during recent seasons (2013/14-2016/17 seasons) prevenzione e controllo dell'influenza: raccomandazioni per la stagione multinational impact of the 1968 hong kong influenza pandemic: evidence for a smoldering pandemic mortality due to influenza in the united states -an annualized regression approach using multiple-cause mortality data trends for influenza-related deaths during pandemic and epidemic seasons impatto dell'epidemia covid-19 sulla mortalità totale della popolazione residente. primo quadrimestre 2020. full text available for download from the istat website avian influenza a viruses differ from human viruses by recognition of sialyloligosaccharides and ganglosides and by a higher conservation of the ha receptor-binding site coronavirus infections -more than just the common cold communication between viruses guides lysislysogeny decisions koilocytosis: a cooperative interaction between the human papillomavirus e5 and e6 oncoproteins fenner and white's medical virology key: cord-317080-kn56oov6 authors: quadri, sayed. a. title: covid-19 and religious congregations: implications for spread of novel pathogens date: 2020-05-07 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.007 sha: doc_id: 317080 cord_uid: kn56oov6 abstract covid-19 pandemic is ravaging the world. one of the principle preventive strategies is practicing social distancing. congregations of the faithful at local and transnational level are strongly recommended by several world religions and religious orders. gathering of large number of people in close approximation could be a fertile ground for the spread of novel pathogens. the refusal to suspend such gatherings could lead to potential widespread dispersal of infections. currently the world is facing an unprecedented global medical emergency in modern history in 21 the form of covid-19 pandemic. the virus seems to hold no bar and continue its march 22 relentlessly across the globe. covid 19 is spread through droplet and basic reproduction rate, a 23 measure of transmissibility of the virus, ranges from 2.24 to 3.58 (zhao et al., 2020) . public 24 gatherings will evidently increase transmission and therefore social distancing was touted as the 25 foremost preventive strategy.  suspension of communal gatherings must be promptly done as a preventive strategy 196 whenever novel pathogens emerge, in order to contain its spread.  an international regime of containment measures with regards to suspension of religious 198 congregations during infectious disease outbreaks must be devised. iskcon reports 21 coronavirus cases, 5 deaths in uk, all had attended funeral 176 gathering ultra-orthodox jews hit disproportionately hard by israel's coronavirus 180 outbreak preliminary estimation of the basic reproduction number of novel 185 coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the 186 early phase of the outbreak key: cord-320829-uepneyug authors: he, zhongping; zhao, chunhui; dong, qingming; zhuang, hui; song, shujing; peng, guoai; dwyer, dominic e. title: effects of severe acute respiratory syndrome (sars) coronavirus infection on peripheral blood lymphocytes and their subsets date: 2005-08-10 journal: int j infect dis doi: 10.1016/j.ijid.2004.07.014 sha: doc_id: 320829 cord_uid: uepneyug introduction: severe acute respiratory syndrome (sars) caused large outbreaks of atypical pneumonia in 2003, with the largest localized outbreak occurring in beijing, china. lymphopenia was prominent amongst the laboratory abnormalities reported in acute sars. methods: the effect of sars on peripheral blood lymphocytes and their subsets was examined in 271 sars coronavirus-infected individuals. results: there was a significant decrease in the cd45+, cd3+, cd4+, cd8+, cd19+ and cd16+/56+ cell counts over the five weeks of the sars illness although cd4+/cd8+ ratios did not change significantly. the lymphopenia was prolonged, reaching a nadir during days 7–9 in the second week of illness before returning towards normal after five weeks, with the lowest mean cd4+ cell count of 317 cells × 10(6)/l at day 7, and cd8+ cell count of 239 cells × 10(6)/l at day 8. patients with more severe clinical illness, or patients who died, had significantly more profound cd4+ and cd8+ lymphopenia. discussion: lymphopenia is a prominent part of sars-cov infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. possible reasons for the sars-associated lymphopenia may be direct infection of lymphocytes by sars-cov, lymphocyte sequestration in the lung or cytokine-mediated lymphocyte trafficking. there may also be immune-mediated lymphocyte destruction, bone marrow or thymus suppression, or apoptosis. most early reports classified cases as sars on the basis of clinical case definitions, although the recognition of the sars-cov as the causative agent allowed specific laboratory confirmation to be made. [2] [3] [4] [5] [6] [7] [8] [9] [10] approximately 75% of patients presenting with sars have a laboratory-confirmed sars-cov infection, 5 with the remainder either having other infectious causes of severe atypical pneumonia or undetected sars-cov infection. among the clinical and laboratory features of sars, a number of hematological abnormalities have been described. prominent amongst these is a total lymphopenia, although in most studies lymphocyte subset analyses were not reported. 4, 6, [8] [9] [10] [11] in this study, an examination of lymphocyte subsets was undertaken in a cohort of 271 laboratoryconfirmed cases of sars. the daily clinical and laboratory findings of 304 sars patients at the ditan hospital in beijing were entered on a pre-designed database. the clinical case definition of probable sars included a fever of 38 8c or higher, cough or shortness of breath, new pulmonary infiltrates on chest radiography, and close contact with a person who is a suspected or probable case of sars. day 1 of illness was defined as the day of onset of fever. blood was collected for sars-cov specific antibody testing from all patients during hospitalization. sars-cov specific igm and igg were detected using an indirect immunofluorescence assay (ifa, euroimmun ag, lubeck, ger-many), sars-cov rna was detected in throat washes, stools and blood using a sars-cov rna fluorescence quantitative rt-pcr assay (shenzhen pj company, shenzhen, guangdong province, china). immunological tests included t, nk and b lymphocyte cell counts by flow cytometry (multit-est cd45percp/cd3fitc/cd4apc/cd8pe trucount four-color kit, multitest cd45percp/cd3fitc/ cd16+56pe/cd19apc trucount four-color kit, bd biosciences, san jose, ca, usa). lymphocyte counts were performed as controls on 51 non-sarsaffected and otherwise healthy individuals. all analyses were performed at a single laboratory. the study was approved by the ethics committee of ditan hospital, beijing, china. patients satisfying the case definition of probable sars were retrospectively classified after discharge into non-severe (122) and severe (149) cases. the non-severe and severe groups were defined according to 'the standard of clinical diagnosis for atypical pneumonia' guidelines listed by the chinese public health ministry on 4 may 2003. the patients in the non-severe group had a fever of 38 8c or higher, a cough or shortness of breath, and new pulmonary infiltrates on chest radiography. the patients in the severe group had in addition at least one of the following features: dyspnea (respiratory rate >30/ minute), hypoxemia (pao 2 <70 mmhg or spo 2 <93% whilst on oxygen at a rate of 3-5 l/minute), acute lung injury/acute respiratory distress syndrome, a chest radiograph showing multifocal involvement over one third of the lung fields (or that developed to 50% in 48 hours), and shock or multiple organ dysfunction syndrome (mods). they also had other underlying diseases, developed a secondary infection or were over 50 years old. patients satisfying the case definition of probable sars were retrospectively classified after discharge into those who recovered (246 cases) and those who died from sars (25). probable sars patients were regarded as laboratory confirmed if they had at least one of the following: sars-cov igg and/or igm antibody detected by ifa three or more weeks after the onset of the illness, and/or sars-cov rna detected by rt-pcr during the first two weeks of illness. in this study, 271/304 (89.1%) patients were laboratory confirmed as having sars, including 148 (55%) with sars-cov detected by rt-pcr on respiratory tract or fecal samples. of the 148 sars-cov rt-pcr positive samples, sars-cov igg was detected in 145 (98%) and sars-cov igm in 117 (79%) using ifa. 12 there were 33/304 (10.9%) that were negative on sars testing. an alternative laboratory diagnosis was made in 27/33, of which the most common were acute influenza b (13 cases) and klebsiella pneumoniae infection (nine cases). the mean age of the 271 laboratory-confirmed sars cases was 36 ae 16 years, with 51 (18.8%) over 50 years of age and nine (3.3%) under 18 years. there were 157 (57.9%) females and 114 (42.1%) males. there were 92 (33.9%) health care workers, including 51 nurses, 30 physicians and 11 others in the cohort. thirty-two patients had underlying health problems, including diabetes (18 cases), cardiac disease (eight cases), malignancy (four cases), chronic airways disease (one case) and chronic renal failure (one case). one hundred and twelve individuals (41.3%) acquired sars in the hospital setting as health care workers, inpatients, or visitors, mostly in the wards of the hospital. a further 62 cases were infected following home exposure, when family members or friends of hospital-associated cases had come into close contact with affected individuals. the lymphocyte subpopulation counts were compared between 696 samples collected from 271 cases of laboratory-confirmed sars patients and 51 controls ( table 1 ). the total lymphocyte counts from sars patients were compared with those from normal individuals, and the lymphocyte counts at each week after the onset of the illness were compared with other weeks of illness and with those from normal individuals. using nonparametric tests there were significant decreases in the cd45+, cd3+, cd4+, cd8+, cd19+ and cd16/56+ counts over each of the five weeks of the sars illness compared to healthy controls, although the cd4+/cd8+ ratio did not change significantly over the course of the illness. the various lymphocyte populations (cd45+, cd3+, cd4+ and cd8+) were below the normal ranges in the first week of the clinical illness, reaching a nadir during the second week before returning towards normal levels. there were significant differences in lymphocyte subset counts between weeks 1 and 2, weeks 2 and 3, weeks 4 and 5, and weeks 1 and 5 (table 1) (figures 1-3) . these observations are further defined in table 2 where the cd45+, cd3+, cd4+, cd8+, cd19+ and cd16/56+ counts on samples collected daily during the first 21 days of sars are listed. the total, cd4+ and cd8+ lymphopenia was most marked at days 7-9 in the second week of the illness. in table 3 the lymphocyte subpopulation counts were compared between those with severe sars (260 samples from 149 patients), non-severe sars (436 samples from 122 patients), and those that recovered (613 samples from 246 cases) or died (48 samples from 25 patients) from sars. the cd45+, cd3+, cd4+, cd8+, cd19+ and cd16/56+ counts were significantly lower (using nonparametric tests) in those patients that died compared to those who recovered, and in those with severe disease compared to those with nonsevere disease. the interaction between the sars-cov and the immune system is complex. in this study, lymphocyte subsets were measured over five weeks in 271 effects of severe acute respiratory syndrome (sars) coronavirus infection 327 figure 3 kinetics of lymphocyte subsets (expressed as mean number of cells â 10 6 /l) measured over the first five weeks of illness in non-severe and severe laboratory-confirmed sars patients, and in otherwise healthy controls. laboratory-proven non-severe and severe cases of sars, where patients either recovered or died. total lymphocyte counts decreased in the first two weeks of illness (the nadir was in week 2) before increasing in the third week and returning to normal levels by the fifth week. peripheral blood lymphocyte subsets (cd45+, cd3+, cd4+, cd8+) were quantitated by dynamic methods in a large cohort of 271 laboratory-proven cases of sars. this study confirms observations of lymphopenia noted in most other series of sars cases. 4, 6, [8] [9] [10] [11] a study in hong kong reported an absolute lymphopenia (<1000 â 10 6 /l) in 98% of patients during the course of their illness, most marked in the second week. 11 the data discussed here extend these observations (and provide the first data from mainland china), showing that the total lymphocyte counts of sars patients were lower than those of normal individuals throughout the clinical course, and that this was more marked in severe disease compared to less severe illness, and in those who died compared to the survivors. a study of 75 patients from the amoy gardens outbreak in hong kong did not find an association of total lymphocyte counts and progression to ventilatory support and intensive care, 10 although there are differences in the progression to acute respiratory distress syndrome (ards), oxygen saturation and gastrointestinal symptoms in these two cohorts. however, an association of lymphopenia with more severe disease was seen in another cohort of sars cases from hong kong. 6 in contrast with other series of adult sars cases, in the study reported here all patients had laboratory evidence of sars-cov infection. in two series totalling 25 children with probable or suspect sars (although only four children had laboratory-proven sars), total lymphopenia was common and more prominent in older children with more severe disease. 13, 14 lymphocyte subsets (cd4+, cd8+, cd19+ and cd16/56+) were also counted in all patients. a significant cd4+ and cd8+ t cell lymphopenia has been observed in the first two weeks of the sars illness in 31 patients, 11 but in this study, a more prolonged cd4+ and cd8+ lymphopenia was noted. cd4+ and cd8+ cells fell by approximately one half in the second week of the illness before returning to near normal by the end of week 5. in addition, patients with more severe disease had lower counts that took longer to rise. the data show that the cd4+ and cd8+ counts were lower in more severely ill patients and in those that died. the cd4+/cd8+ ratios were not significantly different in the various patient groups. cd19+ b lymphocytes were the first lymphocytes to numerically recover after two weeks and their recovery was associated with the appearance of sars-cov specific igg and igm. cd16/56+ nk cells also began to decrease in the first week (although there was a rise in nk cells towards the end of week 1) to their lowest levels during week 4, and had not returned to normal by week 5. lymphopenia is a prominent part of sars-cov infection and lymphocyte counts may be useful in predicting the severity and clinical outcomes. total and subset lymphopenia occurs in other acute (e.g. measles, cytomegalovirus) and chronic (e.g. hiv) viral infections in humans and animals, but lymphopenia has not been a feature of other human coronavirus infections in adults. [15] [16] [17] lymphopenia has been described in some cases of experimental coronavirus 229e infections in humans. 18 a possible reason for the lymphopenia may be that lymphocytes are directly infected and destroyed by sars-cov. however, angiotensin-converting enzyme 2 has been identified as a functional cellular receptor for the sars-cov, a protein that is not expressed on b or t lymphocytes. 19, 20 this would suggest that direct viral invasion and destruction of lymphocytes is not a major cause of the acute lymphopenia in sars, but this requires further study. other possible explanations for the lymphopenia are lymphocyte sequestration in the lung where sars-cov damage is most evident, or cytokinemediated altered lymphocyte trafficking. there may be immune-mediated lymphocyte destruction (lymphocyte depletion has been noted in autopsies of lymph nodes from sars cases), 21 bone marrow or thymus suppression, or apoptosis. apoptosis has been observed in vitro in measles-induced lymphopenia, 22 and coronavirus 229e can cause in vitro apoptosis in monocytes/macrophages. 23 whether different strains of sars-cov have variable effects on immune responses and clinical disease (as occurs with experimental measles in macaques) 24 is unknown. it is possible that the sars-cov-induced immune suppression predisposes to secondary infections, especially in the more severely ill patients, and it is unknown if there are any longer term effects on humoral or cell-mediated immunity following sars. conflict of interest: no conflict of interest to declare. severe acute respiratory syndrome (sars), world health organization communicable disease surveillance and response (csr), world health organization website a novel coronavirus associated with severe acute respiratory syndrome identification of a novel virus in patients with severe acute respiratory syndrome identification of severe acute respiratory syndrome in canada newly discovered coronavirus as the primary cause of severe acute respiratory syndrome coronavirus as a possible cause of severe acute respiratory syndrome a cluster of cases of severe acute respiratory syndrome in hong kong a major outbreak of severe acute respiratory syndrome in hong kong clinical features and short-term outcomes of 144 patients with sars in the greater toronto area clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study haematogical manifestations in patients with severe acute respiratory syndrome: retrospective analysis kinetics of severe acute respiratory syndrome (sars) coronavirus-specific antibodies in 271 laboratory-confirmed cases of sars children hospitalized with severe acute respiratory syndrome-related illness in toronto clinical presentations and outcome of severe acute respiratory syndrome in children rhinovirus and coronavirus infection-associated hospitalizations among older adults coronavirus 229e-related pneumonia in immunocompromised patients an outbreak of coronavirus oc43 respiratory infection in normandy the time course of the immune response to experimental coronavirus infection of man angiotensin-converting enzyme 2 is a functional receptor for the sars coronavirus tissue distribution of ace2 protein, the functional receptor for sars coronavirus. a first step in understanding sars pathogenesis a clinicopathological study of three cases of severe acute respiratory syndrome (sars) functional and phenotypic changes in circulating lymphocytes from hospitalized zambian children with measles in vitro detection of apoptosis in monocytes/ macrophages infected with human coronavirus measles virus infection in rhesus macaques: altered immune responses and comparison of the virulence of six different virus strains key: cord-320860-qt84oicg authors: zhang, aining; leng, yan; zhang, yi; wu, kefan; ji, yelong; lei, shaoqing; xia, zhongyuan title: meta-analysis of coagulation parameters associated with disease severity and poor prognosis of covid-19 date: 2020-09-15 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.021 sha: doc_id: 320860 cord_uid: qt84oicg background to figure out whether abnormal coagulation parameters are associated with disease severity and poor prognosis in patients with 2019 corona virus disease (covid-19). methods a systematic literature search was conducted using the databases pubmed, embase, and web of sciences until april 25, 2020. we included a total of 15 studies with 2277 patients. platelet count (plt), prothrombin time (pt), activated partial thromboplastin time (aptt), d-dimer (d-d) and fibrinogen (fib) were collected and analyzed. the statistical results were expressed the effect measure by mean difference (md) with the related 95% confidence interval (ci). results the plt level of severe patients was lower than that of mild patients, while the levels of pt, d-d and fib were higher than those of mild patients (p < 0.05). the level of aptt had no statistical difference between two groups (p > 0.05). compared to non-icu patients, pt of icu patients was significantly longer (p < 0.05). in non-survivors, pt and d-d were higher, yet plt was lower than survivors (p < 0.05). there was no significant difference in aptt between survivors and non-survivors (p > 0.05). the funnel plot and egger's regression test demonstrated that there was no publication bias. conclusions our data support the notion that coagulopathy could be considered as a risk factor for disease severity and mortality of covid-19, which may help clinicians to identify the incidence of poor outcomes in covid-19 patients. in early december 2019, a new coronavirus named severe acute respiratory syndrome coronavirus 2(sars-cov-2) caused a catastrophic international phenomenon of the respiratory disease covid-19 1 . this is the third serious coronavirus outbreak in less than 20 years, following sars in 2002 and mers in 2012 2 . since the outbreak, this innovative type of pneumonia, far more contagious than sars, has spread rapidly around the world, posing a serious threat to human life and health 3 . confirmed cases have been reported in 216 countries, areas or territories. as of 23 july 2020, a total of 15,012,731 cases, including 619,150 deaths, have been reported worldwide 4 . although about 15% of cases caused by human coronavirus strains are the common cold, sars-cov-2 infection can have a variety of manifestations ranging in severity from influenza to death 2 . therefore, the identification of certain laboratory parameters that could distinguish between severe and non-severe cases, or between high and low risk of death, will help to improve the understanding of the clinical situation 5 . the most common manifestations of covid-19 infection are fever, cough, and progressive dyspnea caused by respiratory infection 6 . emerging evidence suggested that severe covid-19 may be complicated with coagulopathy, and even severe cases may cause disseminated intravascular coagulation (dic) 7 . research report by tang 8 et al. showed that 71.4% of patients who died of coronavirus met isth criteria for dic. however, a recent study suggested that the characteristics of covid-19-associated j o u r n a l p r e -p r o o f coagulopathy(cac) are different from clotting disorders caused by bacterial infections and other diseases. cac usually presents with elevated d-dimer and fibrinogen levels, but there are few abnormalities in the prothrombin time and platelet count during the initial course of the disease 9 . in order to explore the relationship between coagulopathy and the severity and prognosis of the disease, we conducted this meta-analysis to compare the difference in blood coagulation parameters among covid-19 patients. we conducted a systematic review using pubmed, embase, and web of science databases with the keywords "laboratory" in all fields and "covid-19" or "2019 novel coronavirus disease" or "covid-19 pandemic" or "2019 novel coronavirus infection" or "2019-ncov infection" or "2019-ncov disease" or "covid-19 virus infection" or "wuhan coronavirus", between 2019 and present time (i.e., april 25, 2020) , with no language restrictions. the reference lists of selected studies were also checked for identifying additional eligible studies. all included studies were managed by endnotex9.2 software and duplicates were removed. our inclusion criteria included (1) study population: adult patients (>18 years of age) who were laboratory-confirmed or clinically diagnosed as covid-19; (2) study design: cross-sectional study, prospective/retrospective cohort study, case-control study, and randomized controlled trials. our exclusion criteria included (1) asymptomatic patients; j o u r n a l p r e -p r o o f (2) studies without reporting coagulation parameters; (3) systematic reviews, metaanalyses, editorials and other forms not presenting original data. the results of the initial search strategy were first screened by title and abstract to exclude apparently irrelevant articles. remainings were delivered the full text to further screen based on inclusion and exclusion criteria. two reviewers independently examined the literature, and when there was any disagreement, the opinion of a third researcher was sought to resolve it through discussion. two reviewers independently extracted the following data from the included references: patient basic characteristics (age and sex), clinical classification or clinical outcome and coagulation parameters. there were five coagulation parameters included: plt, pt, aptt, d-d and fib. a third researcher checked the data extraction to ensure compliance with our inclusion criteria and the accuracy of the data. continuous variables were presented as mean ± standard deviation (sd). if variables were represented by median and interquartile range (iqr), we used excel software to convert them to the form of mean ±sd. the data was meta-analyzed using revman5.3 software provided by the cochrane collaboration. the statistical results were expressed the effect measure by mean difference (md) with the related 95% confidence interval (ci). heterogeneity analysis of the included studies was carried out by i 2, , an indicator in percentages used to determine whether the fixed effect model or random effect model was applied. "i 2 > 50%" considered the heterogeneity to be statistically significant that the random effect model was adopted for analysis; otherwise, the fixed effect model j o u r n a l p r e -p r o o f was selected. the level of meta-analysis was equal to 0.05. the axis tool 10 was used to score the methodological quality of included studies, which is a critical appraisal tool to assess study design, reporting quality and the risk of bias in cross-sectional studies 11 . the components of the axis tool consist 20 questions, each of which could be answered "yes" (1 point) or "no or don't know/comment" (0 point). a funnel plot was developed using stata12.0 software to assess publication bias. meanwhile, egger's regression test was applied to make a quantitative analysis of publication bias. the initial search identified 1209 potentially relevant citations through pubmed database and 43 through other sources (fig. 1) . after eliminating the duplicated literature as well as reading titles and abstracts, 39 articles were screened out for fulltext assessment. of these, 28 were excluded for reasons listed in fig. 1 . four additional studies were identified by reading the reference lists of the selected documents, thus, the pooled analysis finally included 15 studies 8, 12-25 . we listed the basic characteristics and quality score of each study included in table 1 . all the studies were cross-sectional studies conducted in china, involving a total of 2277 patients with sample sizes ranging from 30 to 449. among them, 7 studies were included to evaluate differences in coagulation function between mild and severe patients, 4 between icu and non-icu j o u r n a l p r e -p r o o f patients and 5 between survivors and non-survivors. all the statistical results were presented in table 2 , as well as visually displayed through the forest plots. (fig. 2 ). (fig. 3) . we evaluated four indicators of plt, pt, aptt and d-d to investigate coagulation function between survivors and non-survivors, included 3, 5, 2, 5 studies respectively. referred to the i 2 value, we used the fixed effect model to compare the differences of plt and pt between the two groups (i 2 =0, 38%, separately) and the random effect model to compare aptt and d-d between the two groups (i=70%, 81%, separately). the statistics showed that plt of survivors was higher than that of non-survivors (fig. 4 ). studies comparing d-d indicator were used to draw a funnel plot (fig. 5) for the analysis of publication bias. the selected researches were distributed in the plot in a basically symmetrical way, indicating that the possible bias was small. for further quantitative analysis, we conducted egger's regression test (p=0.923) and confirmed that there was no significant statistically evidence of publication bias (table 3) . although the mortality rate of this novel coronary pneumonia is lower than that of sars and mers, the risk of severe and critically ill patients progressing to ards and being admitted to icu still remains fairly high 26 . there is an urgent need to identify a few indicators for early diagnosis of disease progression and prognosis in order to provide more appropriate treatment options. studies have shown that the cytokines il-6 and procalcitonin can be used to predict the severity of covid-19 9 33 . the current view is that sars-cov-2 enters host cells through cell surface receptor, ace2. this process leads to local inflammation, endothelial activation, tissue damage, and cytokine release changes that lead to coagulation activation 34, 35 . another perspective is that the virus interferes, directly or indirectly, with the clotting pathways. the susceptibility of these two pathways to coagulation disorders is mainly related to host factors such as age, comorbidities, and degree of lung injury 36 in conclusion, this study demonstrated beneficial of screening abnormal coagulation parameters, such as decreased plt, elevated pt, d-d and fib for predicting the severity and prognosis of covid-19. we suggest clinicians to pay attention to changes in blood coagulation of covid-19 patients and explore their potential guidance for therapy. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. the study does not require ethical approval because the meta-analysis are based on published research and the original data are anonymous. the authors declared that they have no conflicts of interest to this work. we declare that there are no potential conflicts of interest. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. declaration of i declaration of i declaration of i declaration of interest nterest nterest nterests s s s the authors declare 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hypothesis for potential pathogenesis of sars-cov-2 infection-a review of immune changes in patients with viral pneumonia covid-19 and its implications for thrombosis and anticoagulation facing covid-19 in the icu: vascular dysfunction, thrombosis, and dysregulated inflammation thromboprophylaxis: balancing evidence and experience during the covid-19 pandemic analysis of the association between resolution of disseminated intravascular coagulation (dic) and treatment outcomes in post-marketing surveillance of thrombomodulin alpha for dic with infectious disease and with hematological malignancy by organ failure antiviral anticoagulation coagulopathy signature precedes and predicts severity of end-organ heat stroke pathology in a mouse model difference of coagulation features between severe pneumonia induced by sars-cov2 and non-sars-cov2 using heparin molecules to manage covid-2019 coagulopathy in covid-19 antidepressant-warfarin interaction and associated gastrointestinal bleeding risk in a case-control study risk of bleeding with single, dual, or triple therapy with warfarin, aspirin, and clopidogrel in patients with atrial fibrillation key: cord-318315-r6wqywwe authors: memish, ziad a.; almasri, malak; turkestani, abdulhafeez; al-shangiti, ali m.; yezli, saber title: etiology of severe community-acquired pneumonia during the 2013 hajj—part of the mers-cov surveillance program date: 2014-06-23 journal: int j infect dis doi: 10.1016/j.ijid.2014.06.003 sha: doc_id: 318315 cord_uid: r6wqywwe background: pneumonia is the leading cause of hospital admission during the annual islamic pilgrimage (hajj). the etiology of severe pneumonia is complex and includes the newly emerged middle east respiratory syndrome coronavirus (mers-cov). since 2012, the saudi ministry of health (moh) has required screening for mers-cov for all cases of severe pneumonia requiring hospitalization. we aimed to screen hajj pilgrims admitted to healthcare facilities in 2013 with severe community-acquired pneumonia (cap) for mers-cov and to determine other etiologies. methods: sputum samples were collected from all pilgrims admitted to 15 healthcare facilities in the cities of makkah and medina, saudi arabia, who were diagnosed with severe cap on admission, presenting with bilateral pneumonia. the medical records were reviewed to collect information on age, gender, nationality, and patient outcome. samples were screened for mers-cov by pcr, and a respiratory multiplex array was used to detect up to 22 other viral and bacterial respiratory pathogens. results: thirty-eight patients met the inclusion criteria; they were predominantly elderly (mean age 58.6 years, range 25–83 years) and male (68.4%), and all were from developing countries. fourteen of the 38 patients died (36.8%). mers-cov was not detected in any of the samples. other respiratory pathogens were detected in 26 (68.4%) samples. of these, bacterial pathogens were detected in 84.6% (22/26) and viruses in 80.7% (21/26). twenty-one (80.7%) samples were positive for more than one respiratory pathogen and 17 (65.3%) were positive for both bacteria and viruses. the most common respiratory virus was human rhinovirus, detected in 57.7% of the positive samples, followed by influenza a virus (23.1%) and human coronaviruses (19.2%). haemophilus influenzae and streptococcus pneumoniae were the predominant bacteria, detected in 57.7% and 53.8%, respectively, of the positive samples, followed by moraxella catarrhalis (36.4%). conclusions: mers-cov was not the cause of severe cap in any of the hospitalized pilgrims investigated. however we identified a variety of other respiratory pathogens in the sputum of this small number of patients. this indicates that the etiology of severe cap in hajj is complex with implications regarding its management. severe community-acquired pneumonia (cap) is not uncommon during hajj. mandourah and colleagues investigated all critically ill patients, who were of over 40 nationalities, admitted to 15 hospitals in two cities in the 2009 and 2010 hajj seasons. 3 pneumonia was the primary cause of critical illness in 27.2% (123 cases) of all icu admissions and occurred most commonly in the second week of hajj, corresponding to the period of greatest pilgrim density. severe cap accounted for 18.1% of all icu admissions. worldwide, pneumonia is a common illness that is potentially life-threatening, especially in older adults and those with comorbid diseases. 7, 8 the etiology of pneumonia differs between and within countries depending on regional differences in prevalence and types of microorganism, and other factors such as the frequency of use of antibiotics, environmental pollution, awareness of the disease, and life-expectancy of the population. 9 the etiology may also differ depending on whether the pneumonia is community-or hospital-acquired. 7, 8 in this context, the hajj is a special case as it brings a large number of people, many elderly with underlying diseases, from various regions of the world, into close proximity to perform physically exhausting religious rights. these factors, combined with the common use of antibiotics among pilgrims, make the etiology of pneumonia during hajj complex, and hence standard guidelines for the management of the disease may not always work during this mass-gathering event. although many pathogens have been associated with pneumonia, a small range of key pathogens are usually the cause of most cases. 7, 10 in recent years, the middle east respiratory syndrome coronavirus (mers-cov) has also emerged as a cause of serious illness including severe pneumonia. 11 since the first reported case of mers in saudi arabia in 2012, 12 the saudi ministry of health (moh) has set up an ongoing mers-cov surveillance system. as part of this surveillance, it is required that all cases of severe cap with bilateral pneumonia requiring hospitalization are investigated for mers-cov. hence, we used molecular techniques to screen the sputum of hajj pilgrims diagnosed with severe cap requiring hospitalization in 2013 for the presence of mers-cov. other etiologies were also investigated using a respiratory multiplex array to detect bacterial and viral respiratory pathogens. all pilgrims attending the 2013 hajj who were admitted to 15 healthcare facilities in the cities of makkah and medina, saudi arabia, and diagnosed on admission with bilateral pneumonia, were included in the study. the medical records of the patients were reviewed to collect information on age, gender, nationality, and patient outcome. during the period 26 september to 2 november 2013, sputum samples were collected from each patient on admission, prior to any antibiotic therapy. samples were kept refrigerated until processing. mers-cov was detected in the samples using reverse transcriptase polymerase chain reactions (rt-pcr) targeting the region upstream of the e gene (upe) and the open reading frame (orf) 1a (nsp6 protein), as described previously. 13, 14 briefly, nucleic acid was purified from a 200-ml volume of sample using the magna pure lc nucleic acid extraction kit (roche, in, usa). each sample was independently tested with the two rt-pcr assays in a 25-ml reaction containing 5 ml of rna, 12.5 ml of 2x buffer (superscript iii one-step rt-pcr with platinum taq (invitrogen, ny, usa)), 0.4 ml of mgcl 2 (50 mm), 1 ml of forward primer (10 mm), 1 ml of reverse primer (10 mm), 1 ml of probe (5 mm), 3 we collected sputum samples from all pilgrims hospitalized in 15 hospitals of two cities in saudi arabia who were diagnosed with severe cap during the 2013 hajj season. thirty-eight patients fulfilled the inclusion criteria; they were predominantly elderly (mean age 58.6 years, range 25-83 years) and male (68.4%). all patients were from developing countries, the majority of whom (78.3%) were from asia. the nationalities most represented were indonesia (32.4%), pakistan (18.9%), and india (10.8%). of the 38 patients, 30 (78.9%) required icu admission. fourteen (36.8%) patients died, while the remaining patients recovered and were discharged. the mortality rate among those admitted to the icus was 46.6%. mers-cov was not detected in any of the sputum samples. other respiratory pathogens were detected in 26 (68.4%) of the 38 samples, while the remaining samples were negative for the 22 respiratory pathogens in the testing panel (table 1 ). of the positive samples, bacterial pathogens were detected in 84.6% (22/26) and viruses in 80.7% (21/26). twenty-one (80.7%) samples were positive for more than one respiratory pathogen and 17 (65.3%) were positive for both bacteria and viruses. the most common respiratory virus was human rhinovirus, which was detected in 57.7% of the positive amples, followed by influenza a virus (23.1%) and human coronaviruses (19.2%). h. influenzae and s. pneumoniae were the predominant bacteria, detected in 57.7% and 53.8%, respectively, of the positive samples, followed by m. catarrhalis (36.4%). respiratory tract infections are common illnesses during the hajj, 15 and pneumonia is the leading cause of hospital admission, including admission to the icu, during the pilgrimage. [1] [2] [3] [4] 16 for instance, a study of hospital admissions in makkah and mina during the 2002 hajj reported that 39% of hospitalizations were for pneumonia. 16 in the current study, as part of the saudi moh mers-cov surveillance, we investigated the etiology of severe cap in pilgrims attending the 2013 hajj requiring hospitalization. most of the 38 patients were elderly, with a large proportion of males, and all were from developing countries. these observations are similar to those of previous reports investigating pneumonia during hajj. 17, 18 for example, alzeer and colleagues investigated 64 patients admitted with pneumonia to hospitals in the 1994 hajj season. 17 nearly all patients were from developing countries; their mean age was 63 years (range 21-91 years) and 75% were males. the overall mortality rate among the patients we investigated was 36.8%, and among those admitted to icus was 46.6%. internationally, the reported mortality of patients with severe cap requiring icu admission is over 30% and the long-term mortality of cap is between 35.8% and 39.1% at 5 years. 8, 19, 20 our results are in agreement with these figures. a few investigations have reported the mortality rates from pneumonia during hajj. one study 5 during the 1986 hajj season reported a pneumonia case fatality rate of 34%, while another 17 reported a mortality rate of 17% among 64 patients admitted to hospitals in the 1994 hajj season. mandourah and colleagues investigated severe pneumonia during the 2009 and 2010 hajj seasons. 3 pneumonia was community (hajj)-acquired in 66.7% of cases and the overall short-term mortality (during the 3 weeks of hajj) was 19.5%. most patients with diagnosed cap are treated empirically and the role of microbiological testing for patients with cap is still a matter of debate. 7 however there is a clear rationale for establishing the causative agent to allow the optimal selection of agents against a specific pathogen and to limit the misuse of antibiotics and its consequences; it is also important to identify pathogens associated with notifiable diseases such as legionnaires' disease and tuberculosis. 21 the possible involvement of mers-cov is an additional, current, reason. knowledge of the etiological agent of pneumonia-related illness is a challenging step in the management of pneumonia in hajj. [1] [2] [3] 17 in general, the identification of the etiology of cap remains difficult in any setting despite advances in microbiological and serological methods. molecular diagnostic tests for common and atypical causative pathogens of cap are now available and have increased the diagnostic yield and decreased the time required to render results dramatically. [22] [23] [24] although many pathogens have been associated with cap, a small range of key pathogens are the cause of most cases. internationally, the predominant pathogen in cap is s. pneumoniae. 7,10 other causative agents include, but are not limited to, h. influenzae, m. pneumoniae, c. pneumoniae, legionella spp, chlamydia psittaci, coxiella burnetii, enteric gram-negative bacteria (enterobacteriaceae), pseudomonas aeruginosa, staphylococcus aureus, anaerobes, and respiratory viruses (influenza virus, adenovirus, respiratory syncytial virus, parainfluenza virus, coronavirus). 7, 8 the frequencies of other causes, such as mycobacterium tuberculosis, c. psittaci, c. burnetii, francisella tularensis, and endemic fungi (histoplasmosis, coccidioidomycosis, blastomycosis) vary between epidemiological settings. 7 recently, mers-cov has also emerged as a cause of serious illnesses including pneumonia and is the subject of worldwide concern. 11 the primary objective of the study was to determine if mers-cov was the cause of the severe pneumonia in the hospitalized patients. our results indicate that mers-cov was not the etiological agent of the illness. these results support previous reports suggesting that mers-cov has not so far been problematic during hajj. a study conducted during the 2013 hajj, the same year as our study, found no evidence of mers-cov nasal carriage among 5235 hajj pilgrims screened. two reports on french pilgrims during the 2012 and 2013 hajj seasons also reported a lack of mers-cov nasal carriage among the pilgrims screened despite a high rate of respiratory symptoms. 25, 26 we found s. pneumoniae to be prevalent in the sputum samples. this is in accordance with many international reports. 7,10 studies performed during previous hajj seasons have reported the organism as a cause of respiratory tract infections including penumonia. 3, 17, 18 for example, among 395 sputum samples collected from hajjis with respiratory tract infections in 1991 and 1992, s. pneumoniae was detected in 4.8% and 12.3%, respectively. 27 among the 64 patients with pneumonia admitted to two tertiary hospitals in makkah during the 1994 hajj, s. pneumoniae was detected in 9.4% of the cases. 17 3 in addition to s. pneumoniae, other common pathogens identified in our sputum samples were h. influenzae, m. catarrhalis, and viral agents, in particular human rhinovirus, influenza a virus, and human coronaviruses. studies from the gulf corporation council (gcc) states have found similar results. the common pathogens causing cap in gcc states were found to be s. pneumoniae, h. influenzae, and m. catarrhalis. 28, 29 in addition, the importance of atypical pathogens including m. pneumoniae, c. pneumoniae, and l. pneumophila in the etiology of cap in the gcc region has been documented. 28 other etiologies, particularly influenza viruses, varicella zoster virus, and m. tuberculosis, are increasingly recognized as causative pathogens of cap within the region. 28 in the context of hajj, in addition to s. pneumoniae, a number of other organisms have been reported as the cause of pneumonia. these include influenza a (h1n1), 3 m. tuberculosis, 1,3,17,18 s. aureus, 3 fungi such as candida albicans, 3, 18 and gram-negative organisms including p. aeruginosa, l. pneumophila, acinetobacter sp, and members of the enterobacteriaceae family. 3, 17, 18 some, however, have dismissed many of these organisms as more likely to be respiratory tract colonizers rather than the causative agents. 30 in our study, respiratory pathogens were detected in 68.4% of sputum samples (26/38) and 80.7% (21/26) of these were positive for more than one pathogen. this is a higher proportion than that reported previously by asghar et al., who isolated more than one pathogen in only 16.3% of the samples from 76 patients with confirmed cap in the 2005 hajj. 18 in another study, a higher percentage (35%) was reported. 24 the differences in detection rates may reflect the differences in identification methods used in the various studies. our study has some limitations. in addition to mers-cov, our test panel detects a specific set of 22 bacterial and viral respiratory pathogens. this means that other respiratory pathogens including fungi and other viruses and bacteria not included in the panel could have been missed. this may be of importance, as organisms not included in the panel such as m. tuberculosis, enterobacteriaceae, p. aeruginosa, and fungi, have been reported as causative agents of pneumonia during hajj. 3, 17, 18 also, we only used sputum samples for identification, and no microbiological investigations of other samples (e.g. blood) were performed to confirm the cause of pneumonia. finally, some of the organisms identified may have been respiratory tract colonizers and not the causative agents. in this context, a strength of our study is that the sputum samples were obtained on admission and before the start of antibiotic therapy. collecting sputum samples after the start of antibiotic treatment would have been of little value as it would have detected mainly respiratory tract colonizers. in conclusion, we investigated the etiology of severe cap in 38 hospitalized hajj pilgrims. mers-cov was not the cause of pneumonia in any of the patients. however, we detected a variety of pathogens in sputum samples of the patients, with most samples containing more than one agent. this observation, along with previous reports on cap in hajj, indicates that typical pneumonia treatment regimens may not work well during the hajj season due to the wide variety of organisms that may be involved. this may necessitate more active investigations into the causes of pneumonia for identification and sensitivity testing in order to provide optimal treatment and a good outcome. molecular methods can be a quick and sensitive means to determine the possible causative agents. pneumonia is a significant illness during hajj and interventions to reduce its burden during the pilgrimage should be adopted. measures to reduce respiratory tract infections during hajj are already in place. 31 other strategies may include improved respiratory tract infection surveillance and optimization and dissemination of recommendations for adult vaccination. 32, 33 continuous surveillance for mers-cov during hajj and outside the pilgrimage season is crucial to monitor the mers-cov situation in saudi arabia. conflict of interest: no conflict of interest to declare. causes of admission to intensive care units in the hajj period of the islamic year 1424 causes of hospitalization of pilgrims in the hajj season of the islamic year clinical and temporal patterns of severe pneumonia causing critical illness during hajj severe sepsis and septic shock at the hajj: etiologies and outcomes health hazards and risk factors in the 1406 h (1986 g) hajj season comparison of mortality and morbidity rates among iranian pilgrims in hajj community-acquired pneumonia bts guidelines for the management of community acquired pneumonia in adults: update bacteriological and clinical profile of community acquired pneumonia in hospitalized patients the bacterial aetiology of adult community-acquired pneumonia in asia: a systematic review state of knowledge and data gaps of middle east respiratory syndrome coronavirus (mers-cov) in humans isolation of a novel coronavirus from a man with pneumonia in saudi arabia detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction assays for laboratory confirmation of novel human coronavirus (hcov-emc) infections respiratory tract infection during hajj pattern of admission to hospitals during muslim pilgrimage (hajj) tuberculosis is the commonest cause of pneumonia requiring hospitalization during hajj (pilgrimage to makkah) profile of bacterial pneumonia during hajj empiric antibiotic therapy and mortality among medicare pneumonia inpatients in 10 western states patients with community acquired pneumonia admitted to european intensive care units: an epidemiological survey of the genosept cohort practice guidelines for the management of community-acquired pneumonia in adults. infectious diseases society of america diagnostic tests for agents of community-acquired pneumonia molecular diagnostics for detection of bacterial and viral pathogens in community-acquired pneumonia etiology of community-acquired pneumonia: increased microbiological yield with new diagnostic methods lack of nasal carriage of novel corona virus (hcov-emc) in french hajj pilgrims returning from the hajj 2012, despite a high rate of respiratory symptoms lack of mers coronavirus but prevalence of influenza virus in french pilgrims after bacteria and viruses that cause respiratory tract infections during the pilgrimage (haj) season in makkah, saudi arabia microbiology of community-acquired pneumonia in the gulf corporation council states demographics and microbiological profile of pneumonia in united arab emirates aetiological agents of community acquired pneumonia respiratory tract infections during the annual hajj: potential risks and mitigation strategies pneumococcal disease in the arabian gulf: recognizing the challenge and moving toward a solution the potential for pneumococcal vaccination in hajj pilgrims: expert opinion key: cord-323696-0lq8ql6n authors: bearman, gonzalo; pryor, rachel; vokes, rebecca; cooper, kaila; doll, michelle; godbout, emily j.; stevens, michael p. title: reflections on the covid-19 pandemic in the usa: will we better prepared next time? date: 2020-05-20 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.059 sha: doc_id: 323696 cord_uid: 0lq8ql6n abstract the united states (us) spends more on healthcare than any other country with little evidence of better, or even comparable, outcomes. we reflect on the us and the covid-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. these include the us healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of american exceptionalism. without institutionalizing the lessons learned, the us will be positioned to repeat the missteps of covid-19 with the next pandemic. the united states (us) spends more on healthcare than any other country with little evidence of better, or even comparable, outcomes. we reflect on the us and the covid-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. these include the us healthcare delivery model, the defunding of public health, a scarcity of infectious diseases physicians, the market failure of vaccines and anti-infectives and the concept of american exceptionalism. without institutionalizing the lessons learned, the us will be positioned to repeat the missteps of covid-19 with the next pandemic. states of america (us) exceeds 1.2 million infections and 78,000 deaths, the greatest count per country worldwide. 1 we reflect on the us and its response to the covid-19 pandemic and focus on cultural, economic and structural barriers that threaten both current and future responses to infectious diseases emergencies. the us spends more on healthcare than any other country, with little evidence of better, or even comparable, health outcomes. 2 in most developed nations, governments maintain universal access to healthcare services for citizens and coordinate resources across the span of the healthcare system. this central agency is able to effectively plan healthcare services, reduce inefficiency and develop infrastructure and workforce capacity to meet the population needs. 3 conversely, the us relies on a patchwork of public and private payors to finance healthcare delivery. 4 the fragmented us healthcare system also produces fragmented self-interests. health insurance agencies may seek to limit expenditures of insurance plan members in order to remain solvent, will only increase as americans continue lose their jobs due to the financial impact of covid-19. 6, 7 though the federal government has made assurances that healthcare systems will not bill uninsured patients for care related to covid-19, some uninsured patients have still received bills. 8 like many issues related to the american healthcare system, much of an uninsured person's bills are subject to the laws of the individual state in which a person resides. 9 a growing pool of unemployed, uninsured persons will almost certainly impact access to covid-19 testing with negative impact on transmission dynamics. this may result in significant numbers of undiagnosed people with minimal or mild symptoms, not under public health surveillance and contact tracing, transmitting the virus. the fragmentation, disparities in care and misaligned incentives do not provide a strong foundation for public health emergencies. a for-profit business model strives for maximal efficiency and minimal redundancy in supply chain structure. however, the global supply chain "just-in-time" manufacturing is not positioned to support the needs of page 5 of 16 j o u r n a l p r e -p r o o f 5 the healthcare system during a pandemic. this system has forced health care providers to resort to pleas on social media to secure personal protective equipment (ppe). 10 other developed countries, such as finland; effectively prioritized, funded and maintained adequate ppe stockpiles following the cold war, better positioning themselves for the threat of infectious diseases. 11 in the us, the federal government's response to covid-19 including invoking the defense production act (dpa), which requires industries to produce specific products (like ppe) needed to meet critical demands. yet procurement of raw materials for ppe production continues to be challenging for manufacturers. as the pandemic lengthens, supply management organizations increasingly feel severe disruptions. 12 the us federal government waivered on providing the centralized leadership to maximize the effectiveness of the dpa in obtaining raw materials and getting needed products to locations where they are needed most. 13 updating policies like the dpa must be a priority in an increasingly complex global economy. like most aspects of american governance, public health laws and mandates vary from state to state. the centers for disease control and prevention (cdc) provides guidance and recommendations to states but does not provide oversight. the cdc is able to enforce isolation and quarantine for specific communicable diseases in certain circumstances like interstate travel, 14 adequate funding is required to both incentivize id as a career track and to staff both health departments and infection prevention programs. antimicrobial resistance is a public health crisis. estimates predict that 10 million deaths per year related to antimicrobial resistance will occur beginning in 2050, coming at an enormous economic cost. 18 compounding this problem is a paucity of new antimicrobials in development against organisms designated by the world health organization as priority pathogens. 19 although government and non-governmental organizations have created incentives to encourage antibiotic research and development, pharmaceutical companies continue to abandon antibiotic discovery and development efforts. this is largely been because of concerns over a poor return on investment. 20 the current covid-19 pandemic highlights a complex and potentially vulnerable global supply chain for many pharmaceuticals, in addition to ppe. 21 the us has experienced critical supply shortages related to natural disasters in the past. in 2017, in the us, the food and drug administration (fda) oversees clinical diagnostics. at the start of the pandemic, testing was limited to the cdc, which developed and deployed an approved assay to state labs. state labs were unable to validate the assay, leading to significant delays in testing. inconsistent funding of public health programs contributed to covid-19 testing shortages. in late february 2020, the fda approved emergency use authorization allowing private laboratories to produce testing products to meet their diagnostic needs, but test shortages persist despite gradual increases in public and commercial test capacity. both germany and south korea mounted covid-19 responses with more speed, complexity and urgency than the united states. both countries quickly mounted largescale testing capabilities. this was a function of central oversight, coordinated healthcare delivery, public health infrastructure and public trust. within the first two months of diagnosing the first case of covid-19 in south korea, 600 testing sites had been set up, eventually allowing for 20,000 tests each day. 26 high testing volume allows asymptomatic, covid-19 individuals to self-isolate. in addition to testing large swaths of the population, south korean public health officials designed their test to detect the genetic targets recommended by the who. as of may 5, 2020, germany was able to test 120,000 people daily (population 83 million). 27 prior to the arrival of the covid-19 virus in germany, a german lab created a diagnostic test and published a "how to" online for other labs to use. 28 publishing the test "blueprint" allowed other german laboratories to create their own covid-19 tests, maximizing test availability. germany and south korea's responses to the covid-19 pandemic differ in many ways; but widespread, sustained testing allowed for prompt diagnosis, isolation and contact tracing in both countries. j o u r n a l p r e -p r o o f 10 a country's ability to prepare for a novel infectious disease relies on planning, sustaining and executing emergency response systems. this requires emergency preparedness as a national priority. within a loosely integrated and complex combination of private and public healthcare payers, commonly under a for-profit model, supply chain emergency response priorities must be uncoupled from business as usual and supported by state and federal funding. public health systems must be adequately funded and staffed to address both present and future infectious diseases threats. healthcare systems must incentivize infectious diseases and epidemiology as careers for graduates to meet current needs and coming plagues. the slow development of antivirals, antibiotics and vaccines is a market failure requiring robust public-private partnerships for sustained enhancement. will the us be better prepared for the next pandemic? resilience and ingenuity are part of the us cultural fabric, most notably demonstrated in the last century during world war ii. however, resilience and ingenuity are necessary yet not sufficient. without institutionalizing the lessons learned from covid-19, the us will be positioned to repeat the missteps of covid-19 with the next pandemic. the future of us emergency preparedness will reflect the wisdom of us political leader, inventor and intellectual benjamin franklin: "by failing to prepare, you prepare to fail." all named authors have seen and agreed to the submitted version of the paper. this editorial is original work and has not been submitted or published elsewhere. we have no conflicts of interest to report nor did we receive any funding for this editorial. no ethical approval is required by our institution for an editorial submission. higher spending, worse outcomes? the commonwealth fund mirror, mirror 2017: international comparison reflects flaws and opportunities for better u.s. health care. the commonwealth fund. updated july14 shortages resulted with health care providers often resorting to social media to secure personal protective equipment (ppe) what happens when our insurance is tied to our jobs, and our jobs vanish? the washington post up to 43m americans could lose health insurance amid pandemic, report says. the guardian covid-19 coverage for uninsured is underway, but more is needed. the american medical association got coronavirus? you may get a surprise medical bill, too. nbc news with covid-19, some states reopen the aca marketplace for uninsured health in international perspective: shorter lives, poorer health covid-19 survey: impacts on global supply chains. institute for supply management critical supply shortages -the need for ventilators and personal protective equipment during the covid-19 pandemic isn't worried about masks. the new york times legal authorities for isolation and quarantine kaiser family foundation. state data and policy actions to address coronavirus ready or not: protecting the public's health from diseases, disasters, and bioterrorism tackling drug-resistant infections globally: final report and recommendations. review on antimicrobial resistance priority pathogens and the antibiotic pipeline: an update what are the economic barriers of antibiotic r&d and how can we overcome them? coronavirus raises fears of u.s. drug supply disruptions. the washington post the shortage of normal saline in the wake of hurricane maria developing vaccines for sars-cov-2 and future epidemics and pandemics: applying lessons from past outbreaks american orientalism and american exceptionalism: a critical rethinking of us hegemony how is covid-19 affecting south korea? what is our current strategy? the new york times. germany coronavirus map and case count exception? why the country's coronavirus death rate is low. the new york times key: cord-316505-tdlj5smv authors: kumar, abhai; singh, smita; ahirwar, suneel kumar; nath, gopal title: proteomics-based identification of plasma proteins and their association with the host–pathogen interaction in chronic typhoid carriers date: 2013-11-28 journal: int j infect dis doi: 10.1016/j.ijid.2013.10.008 sha: doc_id: 316505 cord_uid: tdlj5smv background: current diagnostic tests are inadequate to detect typhoid cases, as well as the chronic carrier state, the sole reservoir of salmonella enterica serovar typhi. the current study was conducted to find new molecular signatures of pathogen/disease to understand the mechanism behind the host–pathogen interaction in enteric fever. methods: proteomics-based studies were done to determine the expression of differentially expressed proteins in the plasma of controls, acute typhoid cases, and chronic typhoid carriers. further, transcriptome-based analysis using reverse-transcriptase pcr (rt-pcr) was done in controls, acute typhoid cases, and chronic typhoid carriers. results: results showed the upregulation of proprotein convertase subtilisin, furin, haptoglobin, and albumin in the plasma of chronic typhoid carriers. the elevation in mrna expression of four differentially expressed proteins confirms the changes at the transcriptional level. further, the increase in albumin and haptoglobin in chronic typhoid carriers shows their role in free radical generation, inflammation, and monocyte cell signaling. conclusion: through proteomics techniques, this study identified four proteins in the chronic typhoid carrier host that may have a role in the disease pathogenesis of enteric fever. multiple fecal samples shed over the course of a year by the carrier, because of the poor sensitivity of the existing methods of isolation. the test is based on the detection of antibodies against the salmonella lipopolysaccharide (lps) o antigen; flagellar h antigen is more indicative of past and current salmonella infection and not the carrier state. 12 the pcr for typhoid has yielded a sensitivity of >90% using nested primers, but on other hand the dna from uncultured and dead bacteria can also be amplified by pcr, therefore colony-forming units cannot be specifically correlated with the pcr diagnosis. moreover molecular methods for the detection of s. typhi are very technically demanding. 13 proteomics-based methods are currently being employed to increase our understanding of the pathogenesis of enteric fever and to explore the peripheral signatures of enteric fever. 13 the molecular signature can be of host or bacterial origin, or a combination of both, produced during the process of infection. 13 biomarkers for intracellular pathogens, such as tuberculosis, have been developed using proteomics and mass spectrometry. 14, 15 the severe acute respiratory syndrome (sars) protein biomarker has been identified using surface-enhanced laser desorption/ionization time-of-flight (seldi-tof). 15 the present study was conducted to investigate the expression of differentially expressed proteins in asymptomatic chronic typhoid carriers, acute typhoid cases, and healthy controls. two-dimensional (2d) gel electrophoresis and mass spectrometry techniques were used to identify newer proteins that may provide an insight into the host-pathogen interactions after salmonella infection and in further colonization of the host leading to the chronic typhoid carrier state. a transcriptomics-based analysis was further conducted to correlate the changes occurring at the mrna level translated exponentially at the protein level. the results of the present study will provide a better understanding and insight into the mechanism of the pathogenesis of salmonella and allow the development of better diagnostic and therapeutic approaches to enteric fever. bovine serum albumin (bsa), tris-base, acrylamide, n,n 0methylene bisacrylamide, urea, agarose, 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (chaps), sodium dodecyl sulfate (sds), dithioerythreitol (dte), dithiothreitol (dtt), bromophenol blue, ethylenediaminetetraacetic acid (edta), and protease inhibitor cocktail were purchased from sigma-aldrich, usa. bradford reagent was procured from bio-rad, usa, and immobiline ph gradient strips, immobiline ph gradient buffer, and cover fluid were purchased from bio-rad, usa. glycerol, sodium thiosulfate, potassium ferricyanide, silver nitrate, sodium carbonate, formaldehyde, and methanol were procured from merck ltd, india. thiourea, acetonitrile, acetic acid, ammonium bicarbonate, trifluoroacetic acid (tfa), and other chemicals required for the study were procured locally from sisco research laboratory, india. macconkey agar and deoxycholate citrate agar were from hi-media, india, and tgf-b and il-10 elisa kits were from invitrogen corp., usa. the study was designed to collect blood samples from outpatients admitted to sir sundar lal hospital, institute of medical science, banaras hindu university, varanasi. patients were examined by an expert clinician, and those with symptoms resembling enteric fever were directed for routine clinical laboratory tests, including typhidot () and culture. patients were aged between 16 and 65 years and were of both sexes, i.e., male and female. the patients' past clinical histories and treatments were also recorded. blood was collected in an anticoagulant-coated vial by expert clinicians. the controls were selected from healthy volunteers who were apparently healthy and without any symptoms of visible disease. written consent was obtained from each participant. the study design was approved by the institutional ethics committee. blood samples were collected from controls, acute typhoid cases, and chronic typhoid carriers, through venipuncture, into edtacoated commercially available vials. the samples were processed immediately for separation of plasma. the typhidot assay (ab diagnopath pvt ltd, new delhi, india) was performed as per the manufacturer's instructions and results were later confirmed by culture and pcr-based methods. the blood of s. typhi-positive subjects was centrifuged at 250 â g for 20 min at 20 8c; platelet-rich plasma was obtained, which was centrifuged at 1800 â g for 10 min to obtain platelet-free plasma. the plasma was mixed with protease inhibitor cocktail and stored at à70 8c until further use. the protein concentration was measured by bradford's method 16 using bsa as standard. 2d-page was performed using the standard procedure. 17, 18 the rehydration reaction was done by using equal amounts of protein of controls and typhoid patients, about 200 mg, and 150 ml commercial isoelectric focusing rehydration buffer containing 8 m urea, 2% chaps, 0.5% immobilized ph gradient (ipg) buffer, 0.02% bromophenol blue, and 15 mm dtt, along with ipg strip (ph 4-7); the reaction was performed overnight at room temperature and isoelectric focusing was performed in a multiphor ii electrophoresis unit (bio-rad) for 14000 volt h (500 v for 30 min, 1000 v for 10 min, 2000 v for 10 min, 5000 v for 10 min, and 8000 v for the remaining period). ipg strips were equilibrated for 20 min in equilibration buffer containing 6 m urea, 30% glycerol, 2% sds, 0.05 m tris-hcl ph 8.8, and 0.002% bromophenol blue. second-dimension electrophoresis was performed using 12.5% resolving polyacrylamide gel. a broad range of molecular weight markers were run in parallel to the strips during the second dimension to calculate the molecular weight of the proteins of interest. the resulting gels were stained with silver nitrate using the standard procedure. 19 in brief, gels were fixed for 2 h in fixing solution (methanol:acetic acid:water, 50:5:45), transferred into water for 1 h, sensitized in sodium thiosulfate (0.02%) for 2 min, rinsed with water, incubated in silver nitrate (0.1%) for 30 min, and finally rinsed with water. the protein spots in the gels were developed in developing solution containing 2% sodium carbonate and 100 ml of 37% formaldehyde. removal of the developer and addition of 1% glacial acetic acid was used to stop the staining. the 2d gels of controls, acute typhoid cases, and chronic typhoid carriers were compared using imagemaster 2d platinum software. the contrast for background and spots was normalized for every gel. each gel was assigned landmarks following spot matching. the normalized percentage volumes of the spots from individual gels were compared between groups to calculate the percentage change in volume in the acute typhoid and chronic typhoid groups vs. control. the change in percentage volume of spots in the 2d gels of controls and acute typhoid cases and chronic typhoid carriers was calculated, and 2d spots with a significant change in spot volume were used for further analysis. the sample for mass spectrometry was made using the standard procedure, 20 with slight modifications. in brief, silver-stained spots found to be differentially expressed were excised, cut into pieces, and washed with 500 ml water with agitation on a vortex mixer. to remove silver stains, excised spots were incubated with 250 ml of 50 mm sodium thiosulfate and 15 mm potassium ferricyanide for 5 min and washed twice with 500 ml water to remove reducing agents. the excised spots were incubated at 60 8c for 30 min with 500 ml of 100 mm nh 4 hco 3 and 45 mm dtt, followed by cooling; 500 ml of 100 mm iodoacetamide was then added and further incubation carried out for 30 min in the dark at room temperature. excised spots were sliced and equilibrated with 500 ml of 50 mm ammonium bicarbonate in 50% acetonitrile, dehydrated with 500 ml of 100% acetonitrile for 20 min, and air-dried. sliced spots were rehydrated in 30 ml of a solution containing 0.02 mg/ml trypsin and 50 mm ammonium bicarbonate at 4 8c for 60 min. the supernatant was discarded and 30-50 ml of 50 mm ammonium bicarbonate was added to the excised spots; these were incubated at 37 8c for 16-18 h and the supernatant removed. twenty-five to fifty microliters of 1% tfa in 60% acetonitrile was added to the pellet and this was sonicated for 10 min. the supernatant was removed following centrifugation at 12000 â g for 30 s. both the supernatants were mixed, freeze-dried, and concentrated by centrifugal evaporation to dryness. mass spectrometric analysis of samples was done at the centre for genomic applications (tcga), new delhi. in brief, matrix, namely a-cyano-4-hydroxycinnamic acid (chca) matrix, was mixed with the dissolved trypsinized peptide samples. after drying, the peptides were spotted on a ground steel plate and subjected to bruker ultraflex maldi-tof/tof and 2d nano lc-esi-trap (agilent) for mass spectrometric identification. the instrument was equipped with a pulsed nitrogen laser. data acquisition and analysis was performed using flex control and flex analysis/biotools version 2.2 software, respectively. data were acquired in reflectron-positive mode using 15-18% laser power. the maldi and tandem spectra used for protein identification from tryptic fragments were searched against the mascot search engine. mass tolerance and monoisotopic values (100 ppm for peptide mass fingerprint and peptide mass tolerance of 2 da for ms/ms spectra) were used for searching. the probability-based mowse score was calculated in terms of ion score -10*log (p), where p is the probability and the observed match was considered a random event. protein scores were derived from ions as a non-probabilistic basis for ranking protein hits, and proteins identified by maldi-tof and lc-ms were of the expected size based on their position in the gel. rna was isolated from whole blood using trizol reagent. polyadenylated rna was reverse-transcribed using oligo-dt primers and the rt-pcr was performed using an rt-pcr kit (thermo-scientific) in accordance with the manufacturer's protocol. the cdna was synthesized from isolated rna using revertaid minus mu-lv reverse transcriptase under standard conditions, as supplied by the manufacturer. the primer sequences used for this study are given in table 3 . the gene expression of b-actin was evaluated concurrently with haptoglobin, proprotein convertase subtilisin (pc5), furin, and albumin. a total 2-ml aliquot of cdna was added to a final volume of 25 ml of pcr mixture (10 mm tris hcl, 50 mm kcl, 1.5 mm mgcl 2 , 0.5 mm dntp, 0.4 mm primers, 2.5 u taq dna polymerase). the reaction conditions and cycles for amplification of the respective genes are given in table 2 . the pcr products were visualized using agarose gel electrophoresis. the band density was analyzed using a computerized densitometry system (alpha imager system, alpha innotech corporation, south africa). the student's t-test was used for comparisons between the different groups; the data are expressed as the mean ae standard error. the differences were considered statistically significant when the p-value was less than 0.05. the subjects who underwent a clinical examination and who had a previous history of enteric fever were subjected to routine were suspected positive for enteric fever after serological and culture tests. typhidot igg positivity was found in 33/50 (66%) with a history of fever of more than 12 ae 3.0 days and a past history of typhoid fever; these cases were assigned to the chronic typhoid carriers group. typhidot igm positivity was found in 43/50 (86%) cases with a history of fever of 6 ae 3.0 days and with no past history of enteric fever; these cases were assigned to the acute typhoid group. fifty healthy volunteers aged 304 ae 20.12 months (50% female) with no signs of any type of disease and found negative by culture and serological tests were assigned to the control group. details of the patient and control groups are given in table 1 . the plasma proteins from 50 controls, 50 acute typhoid cases, and 50 chronic typhoid carriers were subjected to 2d gel electrophoresis. each set of experiments was reproduced twice and the data analyzed by imagemaster 2d platinum software. figure 1 shows the complete resolution of the proteins on 2d gels. a percentage volume change of spots for the typhoid groups greater than two-fold that of the controls was taken into consideration. the expression of four protein spots was found to be significantly upregulated in chronic typhoid carriers as compared to controls and acute typhoid cases, however very little change was observed between the expression of the four spots in acute typhoid cases as compared to controls. further, the differences in expression of all four spots showed a significant upregulation in cases of chronic typhoid carriers as compared to acute typhoid cases (figure 2 ). mass spectrometric analysis using maldi-tof and lc-ms identified these proteins as proprotein convertase subtilisin, furin, haptoglobin, and albumin ( figure 2 ). maldi mass spectra and the probability plot corresponding to proprotein convertase subtilisin, furin, haptoglobin, and albumin, provided m/z values for each protein; these were used to search proteins in the available protein database. with regard to the ion score (à10*log (p), where p is the probability and the observed match was random), protein scores greater than 33 for proprotein convertase subtilisin, furin, and haptoglobin, and greater than 34 for albumin, were considered significant (p < 0.05). the probability-based mowse score obtained for albumin was 157 (p < 0.05); the score was 143 for haptoglobin, 58 for furin, and 38 for proprotein convertase subtilisin. details of the peptide summary report are given in table 4 , as per the minimum information about proteomics experiment (miape) standard. changes found at the protein level in the controls, acute typhoid cases, and chronic typhoid carriers were further evaluated at the mrna level. the expression of proprotein convertase subtilisin, haptoglobin, and albumin in chronic typhoid carriers was significantly higher compared to those of control and acute typhoid cases (p < 0.01 and p < 0.01, respectively; figure 3 ). further, the expression of furin in cases of chronic typhoid was significantly higher as compared with control and acute typhoid cases (p < 0.05 and p < 0.05, respectively; figure 3 ). however, no significant changes were observed between the acute typhoid cases and the control group in the expression analysis of all genes ( figure 3 ). the diagnosis of s. typhi and s. paratyphi a in chronic typhoid carriers requires special consideration as they are a silent threat to others in the population. 21, 22 there is no gold standard test for the detection of chronic typhoid carriers, but the least invasive and most acceptable is stool culture. 23 although molecular methods such as pcr have been used extensively in the identification of acute typhoid cases, its application in chronic typhoid cases is limited due to the low level of s. typhi bacteremia in blood. [24] [25] [26] 28 bacteriological screening of s. typhi carriers is expensive and logistically difficult to perform, therefore a serological means is of practical importance. 25, 26 in the current study we tried to screen for s. typhi infection in enteric fever cases using bacteriological and serological methods and used 2d gel electrophoresis and mass spectrometry as an alternative method to differentiate chronic typhoid carriers based on alterations in the expression of proteins. when analyzed, the plasma proteome of controls, acute typhoid cases, and chronic typhoid carriers showed significant differences in the expression of four protein spots. mass spectrometry data revealed these spots to be proprotein convertase subtilisin, furin, haptoglobin, and albumin. proprotein convertase subtilisin and furin are enzymes that cause specific proteolysis in a regulatory mechanism for the generation of biologically active proteins. 27 the process of activation is performed by subtilisin and/or kexinrelated enzymes known as proprotein convertases (pcs). these recognize and process precursor proteins at the consensus motif rxr/rr. 29,30 figure 2 . a 2d gel electrophoretogram of plasma proteins from controls, acute typhoid cases, and chronic typhoid carriers after silver staining. (b) graphical representation of the percentage volume changes of spot expression in the control, acute typhoid cases, and chronic typhoid carriers groups; *p < 0.05 for controls vs. chronic typhoid carriers, and # p < 0.05 for acute typhoid cases vs. chronic typhoid carriers in the case of spot 1 (proprotein convertase subtilisin); *p < 0.05 for controls vs. chronic typhoid carriers, and # p < 0.05 for acute typhoid cases vs. chronic typhoid carriers in the case of spot 2 (furin); **p < 0.01 for controls vs. chronic typhoid carriers, and ## p < 0.01 for acute typhoid cases vs. chronic typhoid carriers in the case of spot 3 (haptoglobin); *p < 0.05 for controls vs. chronic typhoid carriers, and # p < 0.05 for acute typhoid cases vs. chronic typhoid carriers in the case of spot 4 (albumin). the role of pcs and furin has been reported in the pathogenesis of gram-negative bacilli and viruses. 31 the release of lps from gram-negative bacteria results in the induction of proprotein convertase subtilisin, which affects the level of lipid and lipoprotein metabolism through regulation of lipid receptors on hepatic cells. 31 the chronic carrier stage and gall stone formation are highly associated, because a cholesterol-rich and lithogenic diet allow biofilm formation. 32 in the present study, an increase in proprotein convertase subtilisin in chronic carriers shows the involvement of chronic inflammation induced by the pathogen in the host and an alteration in lipid metabolism and lipid concentration that might lead to gall stone formation. the formation of gall stones in chronic typhoid carriers and the intake of a cholesterol-rich diet were observed in most of the chronic typhoid carriers in our study. the exploitation of host furin in the activation of bacterial toxin, allowing entry into the host cell, has also been well reported. 48 proteolytic processing by furin is an important determinant of pathogenicity for viruses and bacterial toxins. 34 the presence of furin in the trans-golgi network requires a minimum recognition motif for the optimal processing of various bacterial and viral endotoxins in the disease pathogenesis. 34 the cell-specific type expression of furin is not clear; t-cells predominantly express furin, which activates t-cell-activated genes that modulate an important immunosuppressive cytokine. 48 the increase in furin expression in our study might have some role in the induction of immunosuppressive cytokines. transforming growth factor beta (tgf-b) upregulates the expression of the fur gene, which in turn increases pro-tgfb1 maturation. 35 the roles of proprotein convertase subtilisin and furin in the activation of matrix metalloproteinases (mt-mmp), which are involved in extracellular matrix degradation, are known. 33 an increase in tgf-b upregulates the activity of mt-mmps, and their involvement in different types of cancer is well established. 33 a large cohort study of a typhoid outbreak in 1964 showed a markedly increased risk of gall bladder cancer in chronic carriersas high as 167 times that of non-carriers. 35 the expression of mt-mmp in the stromal component may be essential for the malignant potential of gall bladder cancer. 36 the increase in furin and proprotein convertase subtilisin indicates that after infection with salmonella, these proteins may induce the expression of mt-mmps, which play an important role in cancer invasiveness in gall bladder cancer. 37 typhoid fever can cause anemia by a variety of mechanisms. 38 in acute infection or hepatic dysfunction, there is usually very little change in serum albumin levels, because albumin has a long biological half-life. 39, 40 the level of albumin was upregulated in chronic typhoid cases in our study, and this might be due to an increase in free radicals during salmonella infection; the release of hydroxyl radicals and nitric oxide in cases of salmonella has already been reported. 41, 42 the increase in albumin found mainly in chronic typhoid carriers in the current study might occur in order to counteract the generation of free radicals, because albumin is known to have antioxidant properties during free radical generation in the case of infection. [43] [44] [45] the antagonistic effect of haptoglobin on endotoxin was first demonstrated by baseler and burrell. 46 the effect of haptoglobin on endotoxin-induced cytokine release is not yet known. 47 however, it is evident from past research that haptoglobin enters monocytes and neutrophils and interrupts the intracellular function triggered by intracellular lps. 47 the role of haptoglobin in the modulation of proinflammatory cytokines and antiinflammatory cytokines is debatable and needs further investigation. 47 the present study showed an increase in haptoglobin, which is an acute phase protein, in chronic typhoid carriers, and this might have a significant role in triggering the intracellular signaling of monocytes and neutrophils during typhoid carriage. the role of haptoglobin as a modulator of inflammation in pathological conditions such as respiratory infections and endotoxic shock is already known. 47 thus, increased levels of haptoglobin during typhoid carriage provide the environment for s. typhi to modulate the release of cytokines during infection and to sustain its survival in the host. the data from the present study clearly indicate the role of the proteins identified in chronic typhoid carriers, which have a potential effect in perturbing the host inflammatory response triggered by s. typhi during its carriage. further, the role of these proteins in the intracellular cell signaling of monocytes in chronic typhoid carriers needs further investigation in order to understand the mechanism of the host-pathogen interaction and to develop diagnostic kits and therapeutic drug targets. vs. chronic typhoid carriers, and ## p < 0.01 for acute typhoid cases vs. chronic typhoid carriers in the case of proprotein convertase subtilisin; *p < 0.05 for controls vs. chronic typhoid carriers, and # p < 0.05 for acute typhoid cases vs. chronic typhoid carriers in the case of furin; **p < 0.01 for controls vs. chronic typhoid carriers, and ## p < 0.01 for acute typhoid cases vs. chronic typhoid carriers in the case of haptoglobin; **p < 0.01 for controls vs. chronic typhoid carriers, and ## p < 0.01 for acute typhoid cases vs. chronic typhoid carriers in the case of albumin. typhoid and paratyphoid fever typhoid and paratyphoid fever in travellers precise estimation of the number of chronic carriers of salmonella typhi in santiago, chile, an endemic area gallbladder carriage of salmonella paratyphi a may be an important factor in the increasing incidence of this infection in south asia evolutionary history of salmonella typhi age and sex as factors in the development of the typhoid carrier state, and a method for estimating carrier prevalence quantitative bacteriology of the typhoid carrier state comparison of vi serology and nested pcr in diagnosis of chronic typhoid carriers in two different study populations in typhoid endemic area of india chronic and acute infection of the gall bladder by salmonella typhi: understanding the carrier state 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antioxidants of human extracellular fluids purification of haptoglobin and its effects on lymphocyte and alveolar macrophage responses haptoglobin dampens endotoxin-induced inflammatory effects both in vitro and in vivo t-cell-expressed proprotein convertase furin is essential for maintenance of peripheral immune tolerance the authors acknowledge the university grants commission (ugc), india, for financial help (abhai kumar) and the ministry of food science and technology for a research fellowship (smita singh).ethical approval: written consent was obtained from each participant. the study design was approved by the institutional ethics committee.conflict of interest: the authors declare that they have no conflicts of interest. key: cord-334603-yt2pmxi3 authors: de sousa, eric; ligeiro, dário; lérias, joana r.; zhang, chao; agrati, chiara; osman, mohamed; el-kafrawy, sherif a; azhar, esam i; ippolito, giuseppe; wang, fu-sheng; zumla, alimudin; maeurer, markus title: mortality in covid-19 disease patients: correlating association of major histocompatibility complex (mhc) with severe acute respiratory syndrome 2 (sars-cov-2) variants date: 2020-07-18 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.016 sha: doc_id: 334603 cord_uid: yt2pmxi3 abstract as the 2019 (covid-19) pandemic caused by the novel coronavirus, sars-cov-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. ethnicity has been the focus of attention after data from the united kingdom showed a disproportionate number of deaths among healthcare workers from black, asian and other ethnic minority backgrounds (1). in addition to ethnicity, socio-economic factors, prior vaccinations and exposure to other coronaviruses, other factors need to be considered to explain geographical and regional variations in susceptibility, severity of clinical expression of covid-19 disease and outcomes. in the united states there have been disproportionate covid-19 death rates among african americans at around 2.6 times higher than that of other groups. although these data could be due to multiple cultural and socioeconomic factors an underlying genetic susceptibility to sars-cov-2 infection may be a factor. as the 2019 (covid-19) pandemic caused by the novel coronavirus, sars-cov-2 spreads globally, differences in adverse clinical management outcomes have been associated with associated with age >65years, male gender, and co-morbidities such as smoking, diabetes, hypertension, cardiovascular comorbidity and immunosuppression. ethnicity has been the focus of attention after data from the united kingdom showed a disproportionate number of deaths among healthcare workers from black, asian and other ethnic minority backgrounds (1). in addition to ethnicity, socio-economic factors, prior vaccinations and exposure to other coronaviruses, other factors need to be considered to explain geographical and regional variations in susceptibility, severity of clinical expression of covid-19 disease and outcomes. in the united states there have been disproportionate covid-19 death rates among african americans at around 2.6 times higher than that of other groups. although these data could be due to multiple cultural and socioeconomic factors an underlying genetic susceptibility to sars-cov-2 infection may be a factor. genetic factors were thought to play a causative role in the pathogenesis of the sars outbreak in 2003 in a group of taiwanese patients, where the hla-b*4601 haplotype was associated with severity of sars infection (2) . in hong kong chinese patients a strong association was shown j o u r n a l p r e -p r o o f between hlab* 0703 and hla-drb1*0301 alleles and an increased susceptibility to sars infection (3) . in contrast, l-sign homozygote individuals seem to have a significantly lower risk of sars infection (4) . generally, peripheral blood lymphocytes counts of black americans show lower neutrophil counts and proportionally higher frequency of lymphocytes compared to the rest of the population (5). hla-association studies of sars-cov-1 with hla-ligands for sars-cov-2 have been compiled (6) . the biological and clinical relevance of immune responses to sars-cov-2 requires further discussion: 1. autoimmune associations with covid-19. some individuals with covid-19 experienced neurological symptoms, e.g. guillain barre syndrome (7), suggesting an autoimmune background, which has been associated with mhc alleles (8) . the role of mhc variants in increased susceptibility to infections or, vice versa, immune protection is well known for a number of viral diseases, e.g. the role of mhc alleles in hiv-control, or increased risk for chronic hepatitis b (9). dampens autoimmune responses and confers protection from type i diabetes (10) (11) associated with strong ifn-production. hla-dqb1*06:02 has been selected for increased resistance to yersinia pestis in immigrants from africa to europe, engagement of cd4+ t-cells to hla-dqb1*06:02 leads to increased, pro-inflammatory il-17 production, independent of the mhc class ii presented peptides (12) and confers increased risk to the development of anti-myelin directed autoimmune responses (13) . the haplotypes hla-dr2-dq6, dr4-dq8, and dr3-dq2 accommodate peptides from infectious pathogens to cd4+ t-cells from europeans who survived the bottleneck of different, life-threatening infections prevalent in europe (9). these alleles have also shown to be associated with increased risk for autoimmune diseases, for instance to dietary antigens (celiac disease) (14) in part due to their intrinsic capacity to stimulate stronger il-17 production, that facilitates central nervous system (cns)associated disease manifestations (15) . (33) . we used for this prediction a 33 residue peptide with the mutation site in the middle (vnkitygacpkyvkqntlklatgmrnvpekqtr) and thebest fitting peptide with 15 residues that was predicted to binds to hla-drb1*04:01, is exactly the peptide reported earlier (33) recognized by a flu epitope specific t-cell clone. in contrast, the variant (t314k) peptide does not bind ( table 1) . (40), type 1 diabetes (41, 42) , and lyme disease induced arthritis (43) . drb1*09:01 is associated with early childhood myasthenia gravis (44) . drb3*02:02 is linked to grave's disease (44) , serum igg antibodies to chlamydia pneumoniae with essential hypertension (45) and acute necrotizing encephalopathy (46) in conclusion, there appears to be no selective pressure from mhc class i alleles for sars-cov-2 variants tested. most likely there is selective pressure from mhc class ii alleles in regard to binding of the orf8 (l84s) variants assuming that this mutation may be biologically relevant (25, 26) . this data underlines the need to examine sars-cov-2 variants and mhc-associations along with clinical outcomes, a detailed longtime observation with a particular focus on cns-associated symptoms, particularly in individuals with increased risk to develop autoimmune responses. is ethnicity linked to incidence or outcomes of covid-19? association of hla class i with severe acute 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populations chemistry of peptides associated with mhc class i and class ii molecules structure of a complex of the human alpha/beta t cell receptor (tcr) ha1.7, influenza hemagglutinin peptide, and major histocompatibility complex class ii molecule, hla-dr4 (dra*0101 and drb1*0401): insight into tcr cross-restriction and alloreactivity balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies association of hla-drb1/dqb1 polymorphism with high-risk hpv infection and cervical intraepithelial neoplasia women from shanghai impact of host molecular genetic variations and hiv/hpv co-infection on cervical cancer progression: a systematic review drb1*03/drb3*0101, and drb3*0202 are susceptibility genes for graves' disease in north american caucasians, whereas drb1*07 is protective e6 and e7 gene polymorphisms in human papillomavirus types-58 and 33 identified in southwest china multiple sclerosis and autoimmune 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professor ippolito, sir zumla and prof mohamed osman are co-investigators investigators of the pan-african network on emerging and re-emerging infections (pandora-id-net) funded by the european and developing countries clinical trials partnership the eu horizon 2020 framework programme for research and innovation. sir zumla is in receipt of as uk-nihr senior investigatorship. professor maeurer is a member of the innate immunity advisory group of the gates foundation and his work is funded by the champalimaud foundation. all authors are members of the global cancer and infectious diseases consortium for host-directed therapies: weblink: https://fchampalimaud.org/covid19/aci key: cord-317624-qdzhncs0 authors: choi, min joo; kang, minsun; shin, so youn; noh, ji yun; cheong, hee jin; kim, woo joo; jung, jaehun; song, joon young title: comparison of antiviral effect for mild-to-moderate covid-19 cases between lopinavir/ritonavir versus hydroxychloroquine: a nationwide propensity score-matched cohort study date: 2020-10-27 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.062 sha: doc_id: 317624 cord_uid: qdzhncs0 objectives: we aimed to compare the antiviral effect of hydroxychloroquine (hcq) and lopinavir/ritonavir (lpv/r) in patients with covid-19. methods: nationwide retrospective case-control study was conducted to compare the effect of hcq and lpv/r on viral shedding duration among patients with mild-to-moderate covid-19 using the reimbursement data of national health insurance service. after propensity score matching (psm), multivariate analysis was conducted to determine statistically significant risk factors associated with prolonged viral shedding. results: overall, 4,197 patients with mild-to-moderate covid-19 were included. patients were categorized into three groups: lpv/r (n = 1,268), hcq (n = 801), and standard care without hcq or lpv/r (controls, n = 2128). the median viral shedding duration was 23 (iqr 17–32), 23 (iqr 16–32), and 18 (iqr 12–25) days in the lpv/r, hcq, and control groups, respectively. even after psm, the viral shedding duration was not significantly different between lpv/r and hcq groups: 23 (iqr, 17–32) days versus 23 (iqr, 16–32) days. on multivariate analysis, old age, malignancy, steroid use, and concomitant pneumonia were statistically significant risk factors for prolonged viral shedding. conclusion: the viral shedding duration was similar between hcq and lpv/r treatment groups. there was no benefit in improving viral clearance compared to the control group. transmission by reducing the viral shedding duration, as shown from the effect of oseltamivir for influenza (beigel et al., 2020 , meschi et al., 2011 . owing to the highly transmissible property of sars-cov-2, even asymptomatic and presymptomatic patients have transmitted the virus to their family members and colleagues , gandhi et al., 2020 . moreover, as the pandemic has progressed, the number of deaths in high-risk groups has increased dramatically. therefore, the treatment strategy for covid-19 needs to be approached in two ways: reduction of mortality through combined antiviral therapy for severe patients and blockage of transmission through early antiviral treatment for patients with mildto-moderate cases. in the early pandemic periods, the most hopeful antiviral candidates were hydroxychloroquine (hcq) and lopinavir/ritonavir (lpv/r), which had already been on the market for decades with other indications , sanders et al., 2020 . both candidates were expected to interfere viral replication theoretically , sanders et al., 2020 , and showed good in vitro activity against sars-cov-2 , ul qamar et al., 2020 . under urgent needs, many clinical trials using either candidate have been conducted, but there are still insufficient data to recommend hcq or lpv/r use . furthermore, most studies mainly focused on patients with moderate-to-severe covid-19, and antiviral agents were administered at more than 7 days later from symptom onset (borba et al., 2020 , hung et al., 2020 . it is necessary to comparatively evaluate the effect of viral suppression when the antiviral agent is administered in the early stage of symptom development. if effective for viral suppression, it has a very important meaning in terms of infection control and treatment (gautret et al., 2020 , li et al., 2020 . this study aimed to compare the effect of hcq and lpv/r on the viral shedding duration among patients with mild-to-moderate covid-19 cases using south korea's national health j o u r n a l p r e -p r o o f insurance service (nhis) database. this study used reimbursement data from the national health insurance service (nhis) of south korea for the period from january 12, 2020 to may 15, 2020. the nhis covers 97-98% of the population (51 million people). data included age, sex, dates of admission and discharge, diagnoses coded according to the international classification of disease and related health problems, 10 th edition (icd-10), and prescription of medications covered by nhis. currently, the nhis aggregates datasets for real-time reverse transcriptase polymerase chain reaction (rrt-pcr)-confirmed covid-19 cases from information provided by the epidemiological investigation of korea centers for disease control and prevention (kcdc). all subjects with kcd-7 codes for covid-19 were classified into the 5 categories according to the centers for disease control and prevention (cdc) interim guidance: critical (extracorporeal membrane oxygenation, death), severe (mechanical ventilator), moderate grade 2 (high flow oxygen therapy), moderate grade 1 (oxygen therapy), and mild (remaining laboratory confirmed subjects) (supplementary table 1) . this nationwide retrospective study included patients with laboratory-confirmed covid-19 diagnoses who were discharged during the study period from january 12, 2020 to may 15, 2020. among these, only mild-to-moderate grade 1 patients were included in the analysis, and the effect of lpv/r or hcq use on viral shedding duration was evaluated ( figure 1 ). we strictly included patients with mild or moderate grade 1 covid-19, excluding severe patients for the j o u r n a l p r e -p r o o f following reasons: in severe cases, anti-viral agents might have been administered following late aggravation after initial supportive standard care and hospital stay may have been extended due to complications, although sars-cov-2 rrt-pcr test converted to be negative. furthermore, the following two inclusion criteria should be met: i) adults aged ≥19 years and ii) hospitalization within 1 week after laboratory diagnosis for covid-19. the criteria of ≤1 week from diagnosis to hospitalization is needed to assess the effect of early antiviral treatment. exclusion criteria were as follows: i) concomitant lpv/r and hcq treatment; ii) patients on lpv/r or hcq medication prior to diagnosis; or iii) those who received other antiviral agents thought to be effective against camostat, nafamostat, remdesivir, ribavirin, or interferon) . for patients with multiple episodes of hospitalization, the first admission was only included for the analysis. all included patients were categorized according to lpv/r or hcq exposure: lpv/r-group, hcq-group, and control group (supportive standard care only). lpv/r or hcq use was defined as at least one prescription being recorded in the claim data. data on the prescription of lpv/r, hcq, or other drugs were extracted using drug codes based on the anatomical therapeutic chemical classification in the claim data of the study periods. comorbidities were identified using icd-10 codes entered within 1 year prior to covid-19 diagnosis (supplementary table 2 ). charlson comorbidity index (cci) was also calculated to assess the general health status of study subjects (supplementary table 3) . a subgroup analysis was conducted for mild cases only, moderate grade 1 cases only, and patients with pneumonia (defined as icd-10 codes). we defined patient's length of hospitalization as viral shedding duration, which was assessed using rrt-pcr. this is reasonable, because all covid-19 patients in south korea required undetectable rna from two consecutive nasopharyngeal swab specimens (24 hours apart) to be discharged, according to the regulation of kcdc (choi w. s. et al., 2020) . the data are presented using descriptive statistics for continuous and categorical variables. differences between groups were analyzed with an analysis of variance (anova) for continuous variables and chi-square tests for categorical variables. considering the significant differences in baseline characteristics among study groups, propensity score matching (psm) was taken between two groups to be compared. to compare the viral shedding duration, we created propensity scores for the lpv/r-group, hcq-group, and control group. all sets of propensity scores were estimated via multinomial logistic regression using baseline covariates including age, sex, comorbidities, disease severity, and concomitant pneumonia. to compare the viral shedding duration, three data sets were made (lpv/r-group vs. hcq-group; lpv/r-group vs. control group; hcq-group vs. control group), and each of the sets were propensity score matched in 1:1 proportion. age and sex were perfectly matched, and greedy nearest neighbor matching was used for other covariates on the logit of the propensity score. after psm, multiple linear regression was used to determine statistically significant factors associated with viral shedding duration. variables included in the models were age, sex, comorbidities, disease severity, concomitant pneumonia, concomitant use of steroid, azithromycin or oseltamivir, and elapsed days from laboratory diagnosis to hospitalization. all tests were two tailed, and results were considered statistically significant at p-value <0.05. sas version 9.4 (sas institute inc, cary, nc) was used for the analyses. during study periods, a total of 5,720 covid-19 patients were discharged (or death occurred) in south korea. most cases (>95%) were hospitalized within a day from laboratory diagnosis, and more than 98% were hospitalized within 7 days. regarding disease severity, children and adolescents were milder in severity: 99.1% (214/216) were mild, 1.4% (2/216) were moderate grade 1, and none were moderate grade 2 or severe (supplementary table 4 ). similarly, mild cases accounted for the large portion in adults aged 19-64 year (91.7%, 4037/4402). however, in the elderly, less than two-thirds of cases (59.5%, 656/1102) were mild, while the rest required oxygen therapy; one-third of cases on oxygen therapy required high flow oxygen supply or mechanical ventilation. since the first emergence of covid-19 in south korea, the prescription trend of lpv/r and hcq is shown in supplementary figure 1 . overall, lpv/r and hcq prescription tended to decrease, and preference appeared to change significantly depending on the literature published at that time. sequentially, lpv/r was replaced by hcq and supportive standard care. a total of 4,197 patients with mild-to-moderate grade 1 covid-19 were included in this study. patients were categorized into three different groups: those treated with lpv/r (lpv/rgroup, n=1,268), those treated with hcq (hcq-group, n=801), and those with supportive standard care without hcq or lpv/r (control group, n=2,128) (supplementary table 5 ). there were some significant differences among the three groups in the baseline characteristics. compared to lpv/r or hcq-groups, the control group was significantly younger, had fewer j o u r n a l p r e -p r o o f comorbidities, and included more males. the oseltamivir combination rate was less than 0.5% in all groups. the median time of viral rna shedding was 23 (iqr 17-32) days in the lpv/r-group, 23 (iqr 16-32) days in the hcq-group, and 18 (iqr 12-25) days in the control group. there was no significant difference between the lpv/r-group and the hcq-group, but the viral shedding duration was estimated to be significantly longer in both treatment groups compared to the control group. as the baseline characteristics showed significant difference across the three groups, we computed propensity scores for lpv/r use and hcq use based on age and sex. after psm, most of the baseline characteristics were similar, including comorbidities. however, the disease severity and proportion of accompanying pneumonia were still significantly higher in the lpv/r and hcq-group, especially in the lpv/r-group (table 1) . total dosage of lpv/r was 3,884/971 mg on average, which was considered to have been administered for about 5 days when calculated based on 800/200 mg/day as recommended by the guidelines . hcq was used on average of 2,376 mg, which was equivalent to dosage for 5-6 days, calculated based on 400 mg/day recommended by the guideline. the median time of viral rna shedding was not significantly different between the lpv/r and hcq-group: 23 (iqr, 17-32) days versus 23 (iqr, 16-32) days (table 2) . neither agent shortened the viral shedding duration compared to the control group. on multivariate analysis using propensity score-matched data sets comparing each antiviral group versus control group, lpv/r or hcq still showed a significantly longer viral shedding duration compared to the control group. however, the significance due to the use of antiviral agents disappeared in the subgroup analysis which includes only moderate cases or pneumonia cases (supplementary table 6 , 7). on multivariate analysis using dataset comparing lpv/r and hcq groups, neither of the agents showed a significant difference in terms of the viral shedding duration. the factors that significantly influence the viral shedding duration were age, malignancy, steroid use, and concomitant pneumonia (table 3) . as the elapsed time from diagnosis to hospitalization is longer, in-hospital shedding duration was much shorter. in the subgroup analysis for patients with moderate grade 1 severity or concomitant pneumonia, cardiac disease was identified as a factor that significantly increased the viral shedding duration. currently, no specific antiviral agent is available for the prevention or treatment of covid-19, so drug repurposing has been considered as a promising approach to rapidly identify an effective therapy. hcq and lpv/r are the candidates at the forefront of drug repurposing. this nationwide retrospective study was conducted to evaluate the antiviral effect of hcq and lpv/r in the treatment of patients with mild covid-19 using the nhis reimbursement dataset. in this study, the viral shedding duration of sars-cov-2 was similar between hcq and lpv/r treatment groups. when analyzing the effect of antiviral agents, the timing of antiviral therapy is an important issue to be considered. early (within 7 days from symptom onset) initiation of antiviral therapy may be critical in reducing sars-cov-2 viral load, as previously noted (fu keyaerts et al., 2004 . due to the limitation of our database, it was difficult to know the initiation timing of antiviral treatment in each individual patient; however, the government of south korea had launched a series of aggressive measures to perform tight contact tracing and mass screening tests, which enabled early diagnosis within 3-5 days from symptom onset (ryu et al., 2020) . based on the expert's guideline, most patients were treated within 7 days after symptom development . as shown in this study, >95% were hospitalized within a day from laboratory diagnosis. it took more than 1 week to be hospitalized in only a small number of patients, and those were excluded in this study considering the timing issue. hcq or lpv/r monotherapy showed no benefit for improving viral clearance compared to the control group. the viral shedding duration seemed to be rather prolonged in the treatment groups (median viral shedding duration, 22-23 days in the antiviral treatment groups vs. 18 days in the control group). however, it would be possible that the viral shedding duration in the control group was estimated to be shorter than it really is because of the following reasons. first, community treatment centers (ctc), which were introduced in korea as a measure to efficiently distribute limited medical resources during the declared epidemic starting in early march 2020, could make a bias in the claim database. some patients with mild symptoms were transferred from the hospital to ctcs if they were medically stable but needed to maintain isolation (choi w. s. et al., 2020) . although supportive care is maintained in ctcs, some ctcs might not claim reimbursement due to neglectable medical costs and complex process, potentially contributing to the shortened length of hospitalization in the control group. second, during the earlier period of the covid-19 pandemic in south korea, many mild covid-19 patients diagnosed at the airport quarantine received supportive care without antiviral treatment at the ctc. actually, a majority of them had symptoms for more than a week before traveling, j o u r n a l p r e -p r o o f so the viral shedding duration might have been estimated shorter. in the previous studies including mild covid-19 patients in ctcs, the mean viral shedding duration from symptom onset was 21-24.5 days, which is longer than the results of our control group , noh et al., 2020 . when we compared the viral shedding duration between the hcq or lpv/rgroups and the control group in subgroup analyses including only moderate cases or those with concomitant pneumonia, there was no significant difference, which reflected the selection bias of mild cases who were mainly included in the control groups. one of the most effective treatment strategies would be to stop the viral replication at the beginning, thereby minimizing the peak viral load and shedding duration (chu et al., 2004 . it is unclear why hcq or lpv/r did not show favorable antiviral effect in this study. one possible reason is that a higher dose is required to successfully suppress sars-cov-2 in patients as shown in vitro cytotoxicity test , keyaerts et al., 2004 . in particular, the in vitro antiviral activity of hcq at concentrations commonly used in humans was reported minimal (kang et al., 2020) . insufficient data are available regarding the optimal dose to ensure the safety and efficacy of both drugs for covid-19. another possible reason is the inadequate target tissue concentration of those antiviral agents. lpv/r is an anti-hiv drug, innovated to get high plasma and lymphatic tissue concentration, not lung tissue (freeling et al., 2014) . there are no pharmacokinetic data on respiratory tract concentration of lpv/r. although pharmacokinetic data indicate hcq exhibits extensive tissue distribution, the tissue concentration of the respiratory tract might be variable depending on intestinal resorption and hepatic first-pass metabolism (klimke et al., 2020 , maharaj et al., 2020 . in comparison, there are several encouraging reports of hcq on reducing mortality (arshad et al., 2020 , catteau et al., 2020 , di castelnuovo et al., 2020 , mikami et al., 2020 . the inverse association of hcq with mortality was more evident in elderly, in patients j o u r n a l p r e -p r o o f who experienced more severe manifestation or especially having elevated c-reactive protein. furthermore, the beneficial impact was observed even in the late treatment groups, suggesting that the anti-inflammatory and anti-thrombotic potential of hcq may have had more important role rather than its antiviral properties. on multivariate analysis, old age, malignancy, steroid use, and concomitant pneumonia were identified as risk factors for prolonged viral shedding in this study, consistent with previous studies (fu et al., 2020 , zhou et al., 2020 . old age, comorbidities, and steroid use might blunt the host immune response, thereby promoting viral replication. in the subgroup analyses, chronic neurologic diseases were also associated with increased risk of prolonged viral shedding in the cases with mild covid-19, while cardiovascular disease was identified as a risk factor in the moderate cases or cases with concomitant pneumonia. since ace2, the sars-cov-2 binding receptors, is widely expressed in the various organ including the lungs, heart, and vessels, it is possible that greater number of ace2 receptors-along with blunted host response encountered in many comorbid conditions-might promote viral replication, resulting in prolonged viral shedding. recent studies suggested that the negative outcomes in patients with underlying cerebrovascular disease might be due to elevated expression of ace2 (choi j. y. et al., 2020) . besides prolonged viral shedding, pre-existing cardiovascular diseases were associated with worse outcomes of covid-19 (fu et al., 2020) . although unclear, covid-19 might trigger acute coronary syndrome, arrhythmia, or acute exacerbation of heart failure, similar to influenza viral infection (madjid et al., 2020) . sars-cov-2 itself might induce new cardiac pathology or exacerbation of underlying cardiovascular diseases under the systemic and/or localized inflammatory host response, resulting in cytokine storm in some severe cases (madjid et al., cardiotoxicity might be considered (di girolamo et al., 2018 , nord et al., 2004 . in this study, cardiovascular disease was a significant risk factor for longer hospitalization only in the analyses including the hcq-group. although generally safe when used for approved indications, including autoimmune inflammatory rheumatic diseases or malaria, the safety and benefit of hcq treatment are poorly evaluated in covid-19, and potential safety hazards have been announced recently, especially among severe patients and/or high-dose users (borba et al., 2020 , mehra et al., 2020 . this study has some limitations. first, this was a retrospective cohort study. although large number of cases were included, with propensity score matched for relevant variables, we could not rule out residual confounders. second, we did not compare the viability of sars-cov-2 with the duration of infectivity. this study focused on the comparison of rrt-pcr-based viral clearance between lpv/r and hcq. third, this study did not include cases with severe covid-19, having a limitation in evaluating the potential anti-inflammatory impact of hcq or lpv/r in the prevention of complications and fatality. fourth, environmental factors were not considered in this study. environmental factors such as temperature, humidity and food might influence transmission, severity and mortality of covid-19 (eslami and jalili, 2020, roviello and roviello, 2020) . as the severity of covid-19 and the effect of antiviral treatment may vary by region with different environments, further studies from various countries or regions would be required. fifth, there was significant differences in baseline characteristics between hcq and lpv/r groups. to overcome the differences, this study used psm and subgroup/multivariate analyses. finally, because of the limitation of study design using claim database, data on drug concentration and related metabolic factors were not available. in conclusion, we compared the antiviral effect of lpv/r and hcq in patients with mild-tomoderate covid-19 using a large sample size health insurance database. the viral shedding duration was similar between hcq and lpv/r groups. neither hcq nor lpv/r monotherapy showed benefits in improving viral clearance compared to the control group. given such a limited effectiveness of hcq or lpv/r monotherapy, a combination strategy needs to be considered. in fact, studies have shown beneficial effects when combining ribavirin and interferon rather than lpv/r alone (34), and several combination therapies have been tried. this study protocol was exempted for review by the institutional review board of the korea university guro hospital according to the exemption criteria (irb no. 2020gr0260). we declare no conflict of interest. the same superscript letters indicate non-significant differences between groups based on post-hoc analysis. j o u r n a l p r e -p r o o f interim clinical guidance for management of patients with confirmed coronavirus disease (covid-19) infection control guidlines for healthcare professional about covid-19 national institutes of health (nih) treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalized with covid-19 presumed asymptomatic carrier transmission of covid-19 effect of oral oseltamivir on virological outcomes in low-risk adults with influenza: a randomized clinical trial effect of high vs low doses of chloroquine diphosphate as adjunctive therapy for patients hospitalized with severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection: a randomized clinical trial a trial of lopinavir-ritonavir in 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pharmacologic treatments for coronavirus disease 2019 (covid-19): a review hydroxychloroquine in patients with mainly mild to moderate coronavirus disease 2019: open label, randomised controlled trial structural basis of sars-cov-2 3cl(pro) and anti-covid-19 drug discovery from medicinal plants remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-ncov) in vitro covid-19) weekly epidemiological update factors associated with prolonged viral shedding and impact of lopinavir/ritonavir treatment in hospitalised noncritically ill patients with sars-cov-2 infection factors associated with prolonged viral shedding and impact of lopinavir/ritonavir treatment in hospitalised non-critically ill patients with sars-cov-2 infection prolonged sars-cov-2 viral shedding in patients with covid-19 was associated with delayed initiation of arbidol treatment: a retrospective cohort study lpv/r = lopinavir/ritonavir key: cord-326881-3j2e92dj authors: vassallo, m.; manni, s.; pini, p.; blanchouin, e.; ticchioni, m.; seitz-polski, b.; puchois, a.; sindt, a.; lotte, l.; fauque, p.; durant, j. title: patients with covid-19 exhibit different immunological profiles according to their clinical presentation date: 2020-09-28 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1438 sha: doc_id: 326881 cord_uid: 3j2e92dj objectives a novel beta coronavirus has been identified as responsible for the 2019 coronavirus infection (covid-19). clinical presentations range from asymptomatic cases to acute respiratory distress syndrome with fatal outcome. such a broad spectrum of disease expression calls for an investigation of immune response characteristics. methods we identified subjects admitted for covid-19 in whom a large panel of immunological markers were measured, including band tand nk-lymphocyte phenotypes, t-lymphocyte subpopulation cells and plasma cytokines. patients were divided according to symptom severity during hospitalisation, in those with uncomplicated and complicated infection. differences between groups were analyzed. results seventeen patients were included (mean age: 83 years; 9 women; mean delay of symptoms onset: 4 days). six had uncomplicated infection, while 11 developed complicated forms during the hospitalization. cd10 + b lymphocyte levels were inversely correlated with clinical severity (5.8% vs 2.0%, p = 0.04) and cd10+ levels above 3% were independently associated with uncomplicated forms [odds ratio 0.04 (ci 0.002-0.795, p = 0.034)]. tnf-alpha, il-1, il-6 and il-8 measurements upon admission differed between patients who died and those who survived (p < 0.01 for all comparisons). conclusions in a population of elderly patients recently infected with covid-19, cd10 + b cell levels were inversely correlated with clinical severity. cytokine values upon admission were highly predictive of fatal outcome during hospitalisation. these findings could explain differences in the clinical presentation and allow rapid identification of patients at risk for complications. a cluster of pneumonia cases of unknown origin occurred in wuhan hubei province, china, in december 2019 [1] . the pathogen was then identified as a novel beta coronavirus now named severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and responsible for the so-called 2019 novel coronavirus disease (covid-19) [2] . human-to-human transmission of has been established and the virus has rapidly spread worldwide [3] [4] [5] . the typical clinical presentation described was initially that of an acute respiratory syndrome, but several other clinical signs have since been reported, such as diarrhea, anosmia, confusion and vasculitis [7] [8] [9] [10] [11] [12] [13] [14] . however, clinical expression of covid-19 is extremely variable, with, in some cases, asymptomatic or mild forms [15] , while in other subjects severe forms culminating in acute respiratory distress syndrome (ards) have been described, requiring patients to be transferred to intensive care units. consequently, very high mortality rates have been reported worldwide [16] [17] . among clinical predictive factors for severe forms of covid-19, older age, male gender and obesity are the most described, while correlations between abnormal coagulation and hematological parameters with poor prognosis have been observed [18] [19] . immunity is probably one of the major determinants of clinical outcome, as ards has been associated with a so-called cytokine storm, characterized by an exaggerated and uncontrolled inflammatory response to the virus, potentially resulting in lung injury [20] . this immune response to covid-19 calls for indepth investigation. indeed, lymphocytes subsets and immune response during covid-19 have only been partially studied. qin et al. found lower levels of helper t cells and suppressor t cells in severe patients, but demographic characteristics of severe and non-severe patients were significantly different [20] . moreover, while the induction of a robust cellular immunity is likely essential for efficient virus control, dysregulated t cell and nk cell response may contribute to disease severity [21] . therefore, it is urgent to better elucidate how different immune responses across patients affect the clinical presentation. the aim of this study was to retrospectively analyze the immunological profile of patients at early stages of covid-19 in order to identify potential risk factors for subsequent clinical deterioration. we conducted an observational, retrospective cohort study on patients admitted to the internal medicine and infectious diseases department in cannes general hospital, from march to may 2020, with confirmed covid-19 infection. all patients enrolled in this study were diagnosed and treated according to national guidelines for covid-19. blood samples were collected in accordance with the clinical guidelines for inpatients with covid-19. the study was submitted to the french national institute for health data (institut national de données de santé, reference cnil mr004) and patients gave informed consent for retrospectively collecting data. demographic characteristics, underlying comorbidities, duration of symptoms, clinical signs prior to admission, upon admission and during hospitalisation, laboratory findings during hospital stay and clinical outcome were collected from patients' medical records. among laboratory findings, we focused particularly on immunological markers, which were mainly prescribed as a consequence of initial lymphopenia by the -subjects with complicated illness, in case patients experienced severe forms, either already at the admission, or during the hospitalization. severity was defined by signs of pneumonia associated with at least one of the following additional criteria: respiratory rate > 30 breaths/minute, severe respiratory distress, or spo2 < 90% on ambient air. in case of patient transfer to another clinical setting, files were reviewed and physicians interviewed in order to confirm that no significant changes in clinical presentation had been observed for each patient. [24] . the treg gating strategy was based on the gating of cd3+cd4+ and cd3+cd8+ lymphocytes, the cd127wkcd25+ gate being set on cd3+cd4+ t cells using the cd3+cd8+ t cells as a negative control [25] . in addition to expression of cd10, cd20 kappa and lambda on b cells, at least 6 different b cell populations were identified in each sample, namely naive b cells, switched memory b cells, marginal zone-like memory b cells and cd27-negative memory b cells, transitional b cells and plasmablasts. in plasma, cytokine measurement included il-6, il-1, il-8 and tnf-alpha, measured with custom-designed cartridges ella (proteinsimple), following the manufacturers' instructions. categorical variables were described as frequency rates and percentages, while continuous variables were detailed with mean, median and inter-quantile range (iqr). patients with asymptomatic or mild forms were compared to those with moderate-to-severe forms. χ2-tests and student's t-tests were performed to compare variables, and independent risk factors were identified by multivariate analysis. variables with p ≤ 0.20 in univariate analysis were initially selected for the multivariate model and only those with p ≤ 0.05 were retained in the final model. all analyses were performed using statview© software. from february to mai 2020, 101 patients were admitted to our department for covid-19. in a population of elderly patients at a very early stage of covid-19, we found that levels of cd10+ b lymphocyte cells were predictive of the clinical severity. in humans, cd10 is expressed on b cell progenitors in the bone marrow and subsequently disappears gradually with maturation, except on activated germinal center founder b cells, co-expressed with cd27 [27] . these activated b cells are also detected in peripheral blood, the majority of them consisting in immature/transitional b cells [28] . as cd10 is a marker known to be associated with immature/transitional cells, we compared transitional b cells between the two groups, which only revealed a trend (data not shown). our study, which was not intended to specifically analyze this cell population, does not allow to conclude on the origin of these cells and their significance in covid-19 infection, as the difference in levels of transitional cells was not statistically significant between the two groups. however, several hypotheses can be put forward: if they are not immature/transitional cells, they could be activated precursor b cells with early ig rearrangement in order to produce a broad repertoire of antibodies capable of responding to the viral infection [21, 29] . indeed, a robust b-cell response and plasmablasts expansion is generally detected early during sars-cov-2 infection [30] . for reasons that still require investigation, only subjects who produce higher levels of precursors b-cells appear to develop less severe forms of covid-19. besides, ho et al. showed that in hiv-infected patients with advanced disease there is an increased production of cd10+ cells, which are highly susceptible to intrinsic apoptosis, due to overexpression of the anti-apoptotic bcl-2 and bcl-x l proteins [26] . thus, increased levels of cd10+ in patients with mild forms of infection could also be explained by their better ability to eliminate the virus as a consequence of a proapoptotic profile of b lymphocytes and accelerated cell turnover. unfortunately, the analysis did not include il-7 which has been associated with the homeostatic compensation of overrepresented precursor b cells [31] . finally, another explanation for lower levels of cd10+ cells in complicated forms could be a vigorous virally-induced immunosuppression, responsible for a blunted lymphocyte response [32] . if confirmed by larger studies, this work could furnish new insights about the immunological mechanisms of response to the virus and the broad spectrum of clinical presentation in a population at high risk of complication. interestingly, no difference between groups was found upon admission for values of the main plasma cytokines involved in the so-called "cytokine storm". however, although the majority of patients had a mild clinical presentation upon admission, initial cytokine values were highly predictive of fatal outcome during hospitalisation. these results could have another important consequence for future management of covid-19, suggesting that cytokine levels at entry could allow rapid identification of subjects who, despite moderate clinical symptoms, j o u r n a l p r e -p r o o f could be at risk for developing severe complications, and could thus be anticipated to benefit from anti-inflammatory strategies [33] . to our knowledge, this is the first study to evaluate the immunological profile of patients preceding their clinical deterioration. as previously cited, lymphocyte subsets during covid-19 have been already studied by qin et al. [20] , but demographic characteristics of severe and non-severe patients, in contrast with ours, were significantly different between groups. moreover, although time since symptoms onset is not described, we presume that patients were in a later stage of infection than in our cohort, as the immunological analysis was performed when patients already had signs of severity. the study was not designed to determine the role of hydroxycholoroquine regarding clinical response, as only subjects with severe forms received this compound. only randomized prospective studies on recently infected patients can be expected to establish its role. this study is limited by its retrospective character. however, files were systematically reviewed in order to confirm all described clinical data. duration of infection might be another limitation, as it cannot be coincident with symptoms onset. we therefore cannot exclude a difference in duration of viral replication between the two groups. only through systematic and prospective nasal swabs in asymptomatic subjects would it be possible to exactly determine the time of onset of infection. in conclusion, our work shows that levels of cd10+ b cells are higher in patients with uncomplicated covid-19 and that levels of cytokines at the early phase of infection are predictive of a poor outcome, arguing in favor of rapid interventional strategies for patients at risk. this work did not require any funding the study was submitted to the french national institute for health data (institut national de données de santé, reference cnil mr004) and patients gave informed consent for retrospectively collecting data. j o u r n a l p r e -p r o o f there are no conflict of interest to declare clinical features of patients infected with 2019 novel coronavirus in wuhan severe acute respiratory syndrome-related coronavirus: the species and its viruses-a statement of the clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china epidemiologic and clinical characteristics of novel coronavirus infections involving 13 patients outside wuhan, china novel wuhan (2019-ncov) coronavirus clinical characteristics of 145 patients with corona virus disease diarrhea during covid-19 infection: pathogenesis, epidemiology, prevention, and management olfactory dysfunction in coronavirus disease 2019 patients: observational cohort study and systematic review covid-19 and anosmia: a review based on up-to-date knowledge the emerging spectrum of cardiopulmonary pathology of the coronavirus disease 2019 (covid-19): report of 3 autopsies from houston, texas, and review of autopsy findings from other united states cities the neurology of covid-19 revisited: a proposal from the environmental neurology specialty group of the world federation of neurology to implement international neurological registries covid-19, sars and mers: a neurological perspective asymptomatic sars coronavirus 2 infection: invisible yet invincible surviving sepsis campaign: guidelines on the management of critically ill adults with coronavirus disease 2019 (covid-19) management of critically ill patients with covid-19 in icu: statement from front-line intensive care experts in wuhan epidemiological and clinical predictors of covid-19 mild versus severe covid-19: laboratory markers dysregulation of immune response in patients with covid-19 in wuhan, china immunology of covid-19: current state of the science clinical management of covid-19 standardization of flow cytometric immunophenotyping for hematological malignancies: the franceflow group experience cytometry a standardizing immunophenotyping for the human immunology project cd127 expression inversely correlates with foxp3 and suppressive function of human cd4+ t reg cells two overrepresented b cell populations in hiv-infected individuals undergo apoptosis by different mechanisms appearance of immature/transitional b cells in hiv-infected individuals with advanced disease: correlation with increased il-7 identification and characterization of circulating human transitional b cells ig gene rearrangement steps are initiated in early human precursor b cell subsets and correlate with specific transcription factor expression covid-19 and the path to immunity administration to humans leads to expansion of cd8 + and cd4 + cells but a relative decrease of cd4 + t-regulatory cells the role of cytokines including interleukin-6 in covid-19 induced pneumonia and macrophage activation syndrome-like disease current status of potential therapeutic candidates for the covid-19 crisis we wish to thank all the nurses of the department of internal medicine/infectious diseases, without whom this work would not have been possible.a special thank also to nathalie doux and to aurelie leguillermic for the work organization and to brigitte dunais for reviewing this paper.j o u r n a l p r e -p r o o f key: cord-340279-bq5owwot authors: espíndola, otávio de melo; siqueira, marilda; soares, cristiane nascimento; lima, marco antonio sales dantas de; leite, ana claudia celestino bezerra; araujo, abelardo queiroz campos; brandão, carlos otávio; silva, marcus tulius teixeira title: patients with covid-19 and neurological manifestations show undetectable sars-cov-2 rna levels in the cerebrospinal fluid date: 2020-06-04 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.123 sha: doc_id: 340279 cord_uid: bq5owwot abstract we report that patients with covid-19 displaying distinct neurological disorders have undetectable or extremely low levels of sars-cov-2 rna in the cerebrospinal fluid, indicating that viral clearance precede the neurological involvement. this finding points to the need for the development of more sensitive molecular tests and the investigation of other neurotropic pathogens to exclude concurrent neuroinfection. 1 1 highlights 2 • sars-cov-2 rna is mainly undetectable in the cerebrospinal fluid. 3 • sars-cov-2 clearance in the cerebrospinal fluid may precede the neurological involvement. 4 • common neuropathogens should be investigated in the csf of covid-19 patients. (table 1) . csf analysis showed normal to mild elevated protein levels, and 86 pleocytosis was particularly observed in the cases of meningoencephalitis (table 2) . indeed, cns 87 infiltrate was predominantly constituted by mononuclear cells, which is compatible with viral infection 88 (table 2) (table 1) status of sars-cov-2 in 127 cerebrospinal fluid of patients with covid-19 and stroke guillain-barré syndrome related 130 to covid-19 infection two patients with 132 acute meningo-encephalitis concomitant to sars-cov-2 infection management of viral central 134 nervous system infections: a primer for clinicians guillain-barré syndrome as 137 a complication of sars-cov-2 infection plasmapheresis treatment in covid-19-139 related autoimmune meningoencephalitis: case series neurologic features in severe 141 sars-cov-2 infection key: cord-292256-jp80u828 authors: moriguchi, takeshi; harii, norikazu; goto, junko; harada, daiki; sugawara, hisanori; takamino, junichi; ueno, masateru; sakata, hiroki; kondo, kengo; myose, natsuhiko; nakao, atsuhito; takeda, masayuki; haro, hirotaka; inoue, osamu; suzuki-inoue, katsue; kubokawa, kayo; ogihara, shinji; sasaki, tomoyuki; kinouchi, hiroyuki; kojin, hiroyuki; ito, masami; onishi, hiroshi; shimizu, tatsuya; sasaki, yu; enomoto, nobuyuki; ishihara, hiroshi; furuya, shiomi; yamamoto, tomoko; shimada, shinji title: a first case of meningitis/encephalitis associated with sars-coronavirus-2 date: 2020-04-03 journal: int j infect dis doi: 10.1016/j.ijid.2020.03.062 sha: doc_id: 292256 cord_uid: jp80u828 novel coronavirus (sars-coronavirus-2:sars-cov-2) which emerged in wuhan, china, has spread to multiple countries rapidly. we report the first case of meningitis associated with sars-cov-2 who was brought in by ambulance due to a convulsion accompanied by unconsciousness. he had never been to any foreign countries. he felt generalized fatigue and fever (day 1). he saw doctors nearby twice (day 2 and 5) and was prescribed laninamivir and antipyretic agents, his family visited his home and found that he was unconsciousness and lying on the floor in his vomit. he was immediately transported to this hospital by ambulance (day 9). under emergency transport, he had transient generalized seizures that lasted about a minute. he had obvious neck stiffness. the specific sars-cov-2 rna was not detected in the nasopharyngeal swab but was detected in a csf. antihsv 1 and varicella-zoster igm antibodies were not detected in serum samples. a brain mri showed hyperintensity along the wall of right lateral ventricle and hyperintense signal changes in the right mesial temporal lobe and hippocampus, suggesting the possibility of sars-cov-2 meningitis. this case warns the physicians of patients who have cns symptoms. novel coronavirus (sars-coronavirus-2:sars-cov-2) emerged in december 2019 in wuhan, china, and has become a global health emergency. (wang et al., 2020a,b) a preliminary report warned that sars-cov-2 could have neuroinvasive potential because some patients showed neurologic symptoms such as headache, nausea, and vomiting . in order to end the pandemic of sars-coronavirus-2 diseases, the diagnosis of the disease must be prompt and not overlook any findings. this brief report describes the first case of the patient, which brought in by the ambulance due to a convulsion accompanied by unconsciousness, was diagnosed with aseptic encephalitis with sars-cov-2 rna in cerebrospinal fluid. a 24-year-old man he has never been to foreign countries. he felt headache, generalized fatigue and fever in late february 2020 (day 1). on day 2, he consulted a doctor nearby. there, he was prescribed laninamivir and antipyretic agents under the diagnosis of influenza due to his clinical symptoms in spite of the negative result of the diagnostic test. three days later (day 5), he visited another clinic because of the worsening of his previous symptoms, headache, and sore throat. he underwent chest x-ray examination and blood test resulted in negative findings. on day 9, he was found lying on the floor with consciousness disturbance. he was immediately transferred to our hospital by ambulance. during emergency transport, he presented with transient generalized seizures for about a minute. upon arrival at our hospital, he had a glasgow coma scale (gcs) of 6 (e4 v1 m1) with hemodynamically stability. he had obvious neck stiffness. blood investigation showed an increased white cell count, neutrophil dominant, relatively decreased lymphocytes, increased c-reactive protein. subsequent investigations included systemic ct demonstrating no evidence of brain edema. the chest ct showed that there was small ground glass opacity on the right superior lobe and both sides of the inferior lobe. on a further lumbar puncture examination, his cerebrospinal fluid was clear and colorless, and the initial pressure was greater than 320 mmh 2 o. the csf cell count was 12/ml-10 mononuclear and 2 polymorphonuclear cells without red blood cells. anti-hsv 1 and varicella-zoster igm antibodies were not detected in serum samples. the rt-pcr test for sars-cov-2 was performed using a nasopharyngeal swab and csf because we assumed that a sars-cov-2 was involved in the outbreak. although the specific sars-cov-2 rna was not detected in the nasopharyngeal swab, it was detected in csf (supplementary table 1) . during emergency treatment, the endotracheal intubation and mechanical ventilation were required because of multiple epileptic seizures. he was transferred to the icu with the clinical diagnosis of meningitis and viral pneumonia. after the icu admission, he was empirically started on intravenous (iv) ceftriaxone, vancomycin, aciclovir and steroids. he also underwent intravenous administration of levetiraceta for seizure. favipiravir had been administered via nasogastric tube for 10 days since day 2. brain mri was performed 20 h after admission to the icu (figure 1 ). diffusion weighted images (dwi) showed hyperintensity along the wall of inferior horn of right lateral ventricle. fluid-attenuated inversion recovery (flair) images showed hyperintense signal changes in the right mesial temporal lobe and hippocampus with slight hippocampal atrophy. contrast-enhanced imaging showed no definite dural enhancement. these findings indicated right lateral ventriculitis and encephalitis mainly on right mesial lobe and hippocampus. a differential diagnosis was considered to be hippocampal sclerosis accompanying post convulsive encephalopathy. besides, t2-weighted image showed pan-paranasal sinusitis. at day 15, we are continuing treatment for bacterial pneumonia and impaired consciousness due to encephalitis associated with sars-cov-2 in intensive care unit. we declare no competing interests. patient relative's written consent was obtained for publication. clinical specimens for sars-cov-2 diagnostic testing were obtained in accordance with guidelines of national institute of infectious diseases in japan. nasopharyngeal swab specimens were collected with synthetic fiber swabs; each swab was inserted into a separate sterile tube containing 1 ml of phosphate-buffered saline (pbs) supplemented with 0.5% bsa. spinal fluid was collected in sterile specimen containers. specimens were immediately examined at the yamanashi university hospital laboratory department or stored at 4 c until ready for examination. viral rna was extracted from clinical specimen using maglead 6gc (precision system science co., ltd.). the sars-cov-2 rna was detected using agpath-id tm one-step rt-pcr reagents (am1005) (applied biosystems) on cobasz480 (roche). the diagnostic assay for sars-cov-2 has three nucleocapsid gene targets (supplementary materials). the nasopharyngeal swabs obtained from this patient on day 1 (66 minutes after admission) were negative for n and n2 (supplementary table 1 ). as for spinal fluid, however, 1 sample out of 2 (1/2) on day 1 (84 min after admission) was positive for n, but not for n2. therefore, we re-examined the same specimen again and found that 2/2 samples were positive for n, but not for n2. again, the nasopharyngeal swabs were negative for both n and n2. our report described the first case of meningitis/encephalitis associated with sars-cov-2. this case shows the neuroinvasive potential of the virus and that we cannot exclude sars-cov-2 infections even if the rt-pcr test for sars-cov-2 using the patient's nasopharyngeal specimen is negative. in 2002-2003, severe acute respiratory syndrome (sars) pandemic appeared and sars-cov was isolated as the pathogen and as the new family of the human coronaviruses (drosten et al., 2003; ksiazek et al., 2003) . over a number of years, human coronaviruses including sars-cov was identified as possible pathogens for pathologies outside the respiratory systems. (gu et al., 2005; raj et al., 2014) . a report shows that sars-cov genome sequences were detected in the brain of all sars autopsies with real-time rt-pcr (gu et al., 2005) . importantly, the signals were strong in the hippocampus where we found inflammation in the patient's brain. recent study claims that the genomic sequence is similar between sars-cov and sars-cov-2 (yu et al., 2020) , especially the receptor-binding domains of sars-cov is structurally similar to that of sars-cov-2 (lu et al., 2020) . this may lead that sars-cov and sars-cov-2 shares the ace2 as a receptor. that might be the reason why sars-cov and sars-cov-2 might invade the same place in human brains. in the present case, mri demonstrated the abnormal findings of medial temporal lobe including hippocampus suggesting encephalitis, hippocampal sclerosis or post convulsive encephalitis. hippocampal sclerosis would be unlikely because he had no episodes of mesial temporal epilepsy in his past history. in addition, this case was presented with significant paranasal sinusitis. although the relation between sinusitis and retrograde trans-synaptic transfer is obscure, we should pay attention to nasal and paranasal condition in the diagnosis and treatment for sars-cov-2 infection. we claim that this case is important because this case shows that the unconscious patients are potentially infected by sars-cov-2 and might cause the horizontal infection. in order to end the pandemic of sars-cov-2 diseases, the diagnosis of the disease must be prompt and not overlook any findings. finding the suspected patient is the first step of a preventive measure against the pandemic. it should be kept in mind that the symptoms of the encephalitis or cerebropathia may be the first indication, as well as respiratory symptoms, to find the hidden sars-cov-2 patients. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. the authors declare no conflicts of interest. proofreading the manuscript, prof. kohji moriishi for detailed knowledge about coronavirus, prof. zentaro yamagata for ethical considerations, and dr. kenichi matsuda for helpful advice for everything about the medical treatment for the critically ills and discussions over the case. identification of a novel coronavirus in patients with severe acute respiratory syndrome multiple organ infection and the pathogenesis of sars a novel coronavirus associated with severe acute respiratory syndrome the neuroinvasive potential of sars-cov2 may be at least partially responsible for the respiratory failure of covid-19 patients genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding mers: emergence of a novel human coronavirus clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (covid-19) implicate special control measures measures for diagnosing and treating infections by a novel coronavirus responsible for a pneumonia outbreak originating in wuhan the authors would like to thank yamanashi university hospital sars-cov-2 nursing team and respiratory medical team that are fighting against the illness, mr. charles r. allala for carefully supplementary data associated with this article can be found, in the online version, at https://doi.org/10.1016/j.ijid.2020.03.062. key: cord-315059-l6guql8q authors: mubarak, naeem title: corona and clergy: the missing link for an effective social distancing in pakistan. time for some unpopular decisions date: 2020-04-30 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.067 sha: doc_id: 315059 cord_uid: l6guql8q nan countries. to begin with, more than half of the covid-19 cases in malaysia received virus 11 in a congregation of 16000 believers from 30 countries. [1] in iran, for weeks clergy repudiated 12 to ban gatherings of pilgrims in holy shrines till virus crossed the borders of neighbouring 13 countries. [2] tableeghi ijtima (annual, international muslim missionary gathering) in raiwind, 14 pakistan was a super-spreader of the virus due to "stubbornness of the clergy" that opposed 15 closing of the congregation, however, agreed to curtail. later, when the cases surged in the 16 attendees of this congregation, raiwind was completely sealed and declared a hotspot. more 17 than half of the cases in punjab (the mostly affected province) were emanated from raiwind 18 congregation (table 1) pakistan's case is of concern due to a fragile healthcare system, poor hygiene practices, 20 limited access to healthcare, and steep rise in the number of local cases in a population bigger 21 than italy and iran combined. evidence supports the substantial impact of social distancing as 22 a viable practice to contain the spread of the virus. [4] however, successful implementation of 23 any social practice requires public support. in pakistan, the practice of social distancing 24 an evaluation version of novapdf was used to create this pdf file. purchase a license to generate pdf files without this notice. author has no conflict of interest and source of funding to disclose for this manuscript. email: naeem.mubarak@lmdc.edu.pk tel: 00-92-42-37392215 muslim world, and cancelled umrah (pilgrimage). in kuwait, adhan (call for prayer)-an 41 unalterable element in islam since centuries-witnessed a slight change; instead of "hayya 42 alas-salah" (come to prayer), muezzins tweaked, "as-salatu fi buyutikum" (pray in your 43 homes). [6] 44 as who has warned worst is yet ahead [of] us", coming days would be more challenging 45 for pakistan to implement social distancing in the holy month of ramadan (26 th april) when 46 influx in mosques increases many-fold for daily prayers and tarawih (an additional prayer in 47 author has no conflict of interest and source of funding to disclose for this manuscript. email: naeem.mubarak@lmdc.edu.pk tel: 00-92-42-37392215 79 80 none of us have a fear of corona': the faithful at an 57 the new york times. accessed on 25 th sacred ignorance': covid-19 reveals iran split 3-government of pakistan, online covid-19 dashboard interventions to mitigate 66 early spread of sars-cov-2 in singapore : a modelling study covid-19: pakistan to allow mosques prayers in 70 how prayer is changing as a result of covid-19 key: cord-315860-9j667c03 authors: jullien, sophie; pradhan, dinesh; tshering, tashi; sharma, ragunath; dema, kumbu; garcia-garcia, selene; ribó, jose luis; muñoz-almagro, carmen; bassat, quique title: pneumonia in children admitted to the national referral hospital in bhutan: a prospective cohort study date: 2020-04-10 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.017 sha: doc_id: 315860 cord_uid: 9j667c03 objectives: the study aim was to describe the etiological profile and clinical characteristics of pneumonia among children hospitalized in thimphu, bhutan. methods: this prospective study enrolled children aged 2–59 months admitted to the jigme dorji wangchuck national referral hospital with world health organization (who)-defined clinical pneumonia. demographic and clinico-radiological data were collected through questionnaires, physical examination, and chest radiography. blood samples and nasopharyngeal washing were collected for microbiological analysis including culture and molecular methods. results: from july 2017 to june 2018, 189 children were enrolled, of which 53.4% were infants. pneumonia-related admissions were less frequent over the winter. chest radiographies were obtained in 149 children; endpoints included pneumonia in 39 cases (26.2%), other infiltrates in 31 (20.8%), and were normal in 79 children (53.0%). non-contaminated bacterial growth was detected in 8/152 (5.3%) blood cultures, with only two cases of streptococcus pneumoniae. viral detection in upper respiratory secretions was common, with at least one virus detected in 103/115 (89.6%). the three most-commonly isolated viruses were respiratory syncytial virus (52/115; 45.2%), rhinovirus (42/115; 36.5%), and human parainfluenza virus (19/115; 16.5%). a third of patients with viral infections showed mixed infections. case fatality rate was 3.2% (6/189). conclusion: respiratory viral infections predominated among this cohort of who-defined clinical pneumonia cases, whereas bacterial aetiologies were uncommon, highlighting the epidemiologic transition that bhutan seems to have reached. pneumonia is the single largest cause of mortality in children aged under five years, causing an estimated 15.5% of all deaths in children under five years of age, and over 800,000 paediatric deaths annually (liu et al., 2016; un igme, 2018) . most of these lives could be saved through more effective and equitable health system interventions, combining prevention, early and accurate diagnosis, and treatment (walker et al., 2013; rambaud-althaus et al., 2015) . the main pneumonia burden remains disproportionately concentrated in low-and middle-income countries (lmics) in southeast asia and sub-saharan africa (walker et al., 2013) . pneumonia deaths are decreasing, but more slowly than for other major causes of mortality, and too slowly to achieve the sustainable development goal ambition of "ending preventable child deaths" by 2030 (united nations, 2018) . risk factors and causative pathogens of childhood pneumonia differ across the world. obtaining reliable local data, including the burden of the disease, epidemiological trends, and the determination of the main pathogens involved, is imperative to help develop targeted interventions. therefore, adequate surveillance systems are required to monitor the effectiveness of national strategies implemented towards the reduction of the disease burden. however, the lack of local data and weak surveillance systems in many lmics hamper an adequate knowledge of the epidemiology and aetiology of childhood pneumonia in those settings where reliable data are most needed. one country that exemplifies the dearth of data regarding childhood pneumonia is the kingdom of bhutan (jullien et al., 2020) , a small country locked in the himalayas, with an estimated population of 779,666 in 2017 (department of information technology, 2016; ministry of health, 2018) . in this predominantly mountainous country, elevation rises from around 100 m in the southern foothills to over 7500 m in the northern himalayan range, with the capital, thimphu, standing at 2334 m (central intelligence agency, 2019). the climate varies with the altitude, from tropical in the southern plains to alpine with very cold winters in the north. in thimphu, the temperature ranges from à3 c in winter to 22 c in summer on average, coinciding with the monsoon that brings precipitations of around 350 mm in july (climate-data org, 2019). bhutan is classified as a lower-middle income country as of 2020 (the world bank, 2020) . essential health services in both modern and traditional medicines are free for bhutanese citizens, based on a primary healthcare approach (world health organization, 2017) . we conducted this prospective hospital-based observational study to describe the epidemiology, aetiology, and clinical and radiological presentation of world health organization (who)defined pneumonia among children aged between 2 and 59 months admitted to the jigme dorji wangchuck national referral hospital in thimphu. this was a prospective hospital-based study conducted for 12 consecutive months at the jigme dorji wangchuck national referral hospital (jdwnrh) in thimphu. the hospital has 38 paediatric beds, including five in the paediatric intensive care unit (picu). all children aged 2-59 months hospitalized with who-defined pneumonia (irrespective of severity) were eligible for recruitment (world health organization, 2014) (see box 1). children admitted in the preceding seven days or with evidence of a foreign body in the respiratory tract were excluded. potential participants were identified during day and night by the study co-investigators with the collaboration of paediatricians, paediatric residents, and nurses from the outpatient department, the emergency room, the picu, and the paediatric ward. if an eligible participant was missed during the night, the child was assessed and recruited the following morning. all eligible children were recruited provided parent(s) or guardian(s) consented to study participation. on study admission, a study identification number was assigned and a comprehensive physical examination was performed, including anthropometric measurements, vital signs, axillary temperature, and peripheral oxygen saturation in room air. demographic and clinical data were collected from the medical records and through family interviews. sample collection upon enrolment, or as soon as possible after enrolment, included blood samples and nasopharyngeal washing (npw). all the nurses in the picu and paediatric ward were trained at the beginning of the study by the lead investigator on how to collect these samples. when a child was identified for recruitment but blood had already been collected, no further blood sampling was conducted. however, if another blood analysis was clinically indicated, additional blood was obtained for the specific purpose of the study. fluid from pleural effusion was collected when clinically indicated. all recruited patients underwent a postero-anterior chest radiography upon admission. additional information of potential diagnostic interest, such as computed tomography scans, ultrasound, or cerebrospinal fluid investigation available throughout admission, was also collected. children were clinically managed and discharged as per existing hospital protocols and discretion of the treating paediatricians, and were followed-up by one study investigator in terms of outcome determination. all data were collected using digitalized and standardized forms (see supplementary material for clinical definitions and details of variables measured). the who protocol used in clinical trials of pneumococcal conjugate vaccines (pcv) was followed to interpret chest radiographs (cherian et al., 2005) . in brief, readers first judged the box 1. who definitions of pneumonia and severe pneumonia used as inclusion criteria (world health organization, 2014) . history of cough or reported breathing difficulty, and increased respiratory rate (rr) or chest indrawing. severe pneumonia: history of cough or reported breathing difficulty and at least one of the following: oxygen saturation <90% or central cyanosis, severe respiratory distress (e.g. grunting, very severe chest indrawing), signs of pneumonia with a general danger sign: inability to breastfeed or drink, lethargy or reduced level of consciousness, convulsions. increased rr is defined according to age as follows: rr ! 50 breaths per minute in children aged two months or more and less than 12 months. rr ! 40 breaths per minute in children aged 12 months or more and less than 60 months. quality of the film (uninterpretable or interpretable, the latter stratified as suboptimal or adequate) and then classified findings for all interpretable radiographs. significant pathology was defined as the presence of consolidation, other infiltrates, and/or pleural effusion. endpoint radiologically confirmed pneumonia was defined as consolidation, pleural effusion, or both on any hemithorax. initially, two paediatricians independently interpreted the radiographs. discordant results were read by a third reader, trained in who criteria for interpretation of chest radiographs. an additional external quality control measure was included in the study protocol, whereby a paediatric radiologist would read a random sample of 10% of the chest radiographs. however, as substantial discordance was observed between the two primary readers, all chest radiographs were again independently interpreted by the paediatric radiologist using the who criteria. this last reading was accepted as final interpretation for analysis. blood was collected under aseptic conditions following the hospital's validated standardized procedures. blood for haematology, biochemistry, and culture was processed following standard procedures. blood was cultured using an automated blood culture system (bact/alert 1 ). bacterial isolates were identified by colony morphology, growth requirements, and basic biochemical tests. antibiotic susceptibility was determined using disk diffusion in accordance with the guidelines of the clinical laboratory standard institute (clsi, 2015) . additionally, real-time polymerase chain reaction (rt-pcr) for lyta gene of streptococcus pneumoniae in dried-spot collected blood, and host-response biomarkers in additional blood (2 ml, edta tube) were investigated (findings reported elsewhere) (brotons et al., 2017) . the blood samples were centrifuged at 3000 â g for three minutes, and the serum was separated and stored at à80 c. npw samples were homogenized and aliquots frozen at à80 c and subsequently shipped to barcelona, spain, where they were subjected to molecular screening (multiplex rt-pcr qiastat respiratory panel, qiagen, for 17 viral targets and four bacterial targets). npw were also subjected to detection of pneumococcus and capsular typing (findings reported elsewhere). rapid influenza diagnostic tests (alere binaxnow 1 ) were performed as per discretion of the treating clinicians and nurses, independently of the current study. investigations for active tuberculosis included mantoux test and gastric aspirates for microscopy and genexpert 1 . the lead investigator entered data into a computerized password-protected database (odk 1 ) with study identification number. errors in data entry were limited by pre-defined ranges for every value. stata 15.1 was used for data analyses (statacorp, 2017) . mean with standard deviation (sd) and median with interquartile range (iqr) were used to summarize normally and non-normally distributed variables respectively. between 1st july 2017 and 30th june 2018, 1591 children were admitted to the paediatric department of jdwnrh. among them, 286 (18.0%) were children aged 2-59 months with respiratory symptoms, of which 189 (66.1%) were recruited ( figure 1 ). the baseline characteristics of the 189 children are presented in table 1 . median age was 10.8 months; over half of the children were infants. most children were adequately immunized according to age. there was no known case of hiv infection. children were mainly from the district of thimphu, although the study included patients from 16 out of the 20 districts in bhutan. on average, families reported that it had taken around 15 min to reach the closest healthcare facility. twenty-seven children (14.3%) were referred from another health centre. summer, fall, and spring each comprised around 30% of the recruited cases, while winter had the lowest number of pneumonia admissions (10.1%). october was the month with the highest number of cases (37; 19.6%) ( figure 2 ). clinical characteristics upon admission are presented in tables 2 and 3 . wasting (waz à2 sd) was detected in 17 children (9.0%). on admission, 77 children (41.2%) presented with fever, half of the children were breathing fast according to age, and three-quarters were hypoxemic. median basal oxygen saturation was 85% (iqr 80-90) among the 173 children with available measurement in room air without oxygen therapy. on auscultation, typical lung consolidation-related sign (crackles) was most common (57.5%), followed by rhonchi (45.2%) and wheezing (25.0%). on admission, 35.8% of the children were anaemic, 36.9% had leucocytosis, and 25.3% had neutrophilia. two common inflammatory markers were tested at jdwnrh: c-reactive protein (crp) with a mean of 2.06 mg/dl (sd 2.09), and erythrocyte sedimentation rate (esr) with a mean of 24.89 mm (sd 28.02). twenty-five (sanders et al., 2008; bruel et al., 2011) . only four children presented with both high crp and esr. chest radiography was performed in 178/189 children (94.2%). images were available for interpretation by the study investigators in 150 of them (84.3%). in 28 cases, children were discharged before investigators could interpret the radiography findings and the radiograph was missing. one film was judged uninterpretable. among the final 149 readable chest radiographs, 79 (53.0%) were normal, 39 (26.2%) were classified as primary endpoint pneumonia, and 31 (20.8%) as other infiltrates. while hiv infection was not suspected in any child by the treating physicians, active tuberculosis was suspected in 10 children (5.3%) but was not confirmed by the laboratory tests in any of them. blood culture was performed in 148/189 children (78.3%), of which 45 (30.4%) had received antibiotics prior to sample collection (table 4) . thoracocentesis was performed in one child with pleural effusion. six different pathogens were isolated among the eight non-contaminated positive blood cultures: s. pneumoniae (two cases), pseudomonas sp. (two cases), escherichia coli, acinetobacter sp., salmonella typhi, and serratia rubidaea (one case each). drug sensitivity results are shown in supplementary table 2. s. pneumoniae was isolated in the only sample of pleural fluid that was collected, which corresponds to the same child with positive blood culture, subsequently also confirmed by rt-pcr in blood. npw was collected in 129/189 children (68.3%). the npw sample was too scarce or of bad quality to run the test in 14 children (10.9%). among the remaining 115 children, 52 (45.2%) had received antibiotics prior to sample collection. bordetella pertussis was detected in three (2.6%) children, and mycoplasma pneumoniae in one (0.9%) child; chlamydophila pneumoniae and legionella pneumophila were not detected among respiratory samples. at least one virus was identified in 103/115 npw samples (89.6%) ( coronavirus were detected in two children (1.7%). routine rapid flu test was performed under the influenza national surveillance programme in 32/189 children (16.9%), being positive for influenza a in seven cases, for influenza b in one case, and for co-infection of influenza a and b in one case. analysis by rt-pcr confirmed the detection of influenza virus in 4/9 children with positive rapid flu test, and detected 10 additional cases with influenza virus. among children with at least one virus detected, 4/86 (4.6%) had a positive blood culture for bacteria and 24/89 (27.0%) had radiological endpoint pneumonia. among children with no virus detected, 3/9 (23.3%) had a positive blood culture and 4/11 (36.4%) had radiological endpoint pneumonia (supplementary table 3) . no children with influenza had a positive blood culture. however, 6/15 (40.0%) children with influenza identified in their nasopharynx had radiological endpoint pneumonia. lumbar puncture was not indicated in any of the children. children were hospitalized for a median of four days (iqr 2-6) ( table 5) . thirty children required picu admission, with a median stay of 72 h (iqr 24-96). three-quarters of the children were put on oxygen therapy, of which half for at least three days. most children (72.0%) received antibiotics during admission. antibiotics were stopped in the first two days of admission in 10 children (7.4%) and advised to be continued after discharge in 90 (66.2%). main diagnoses given by the treating physician at discharge are shown in supplementary table 4 . half of the children were discharged with a diagnosis of pneumonia or bronchopneumonia. in terms of the seasonal variability of the most common clinical syndromes given by the treating physician at discharge, bronchopneumonia was mainly in fall (50.0%), bronchiolitis in spring (43.6%), and pneumonia did not show a clear seasonal pattern (supplementary figure 1) . six children had a fatal outcome (case fatality rate 3.2%); all had been referred from other centres in critical condition. npw was not collected in three children due to the severity of their illness upon arrival. of the other three children, one child presented a triple co-infection by b. pertussis, parainfluenza virus, and influenza virus. four fatal cases were diagnosed as suffering of pneumonia, and two of bronchiolitis. two deaths occurred within the first 24 h of admission to our centre. a summary of the main characteristics of these six children is presented in supplementary table 5 . abbreviations: gcs: glasgow coma scale; na: not applicable; waz: weight-for-age z-score. a two children presented with convulsions. one was diagnosed as febrile convulsion, while the other child was a severe case of pneumonia which led to a fatal outcome. b some children who presented with non-severe pneumonia developed hypoxemia during their hospitalization, which is a sign of severity as per the who definition. c twenty children (10.6%) did not strictly meet the who definition of pneumonia at the time of admission but were admitted to the paediatric ward with suspected pneumonia or bronchiolitis as per the clinical discretion of the treating paediatricians. four of them developed hypoxemia during hospitalization requiring oxygen therapy and were therefore classified as severe pneumonia. none of the remaining 16 children were admitted to picu or presented other signs of severity, and were classified as nonsevere pneumonia (supplementary table 1 ). d increased respiratory rate (rr) according to age is defined as rr ! 50 bpm in children aged 2-12 months and rr ! 40 bpm in children aged !12 months. this is the first published series of comprehensive epidemiological, clinical, and microbiological data describing bhutanese children under five years of age hospitalized with who-defined clinical pneumonia. mortality related to pneumonia was 3.2%, similar to other studies from lmics (jroundi et al., 2014; lazzerini et al., 2016; bénet et al., 2017; chen et al., 2018; o'brien et al., 2019) . nevertheless, this remains high for bhutan in spite of the country offering free and easily accessible healthcare services. the six children who died were referred from other health centres and reached the study hospital in critical condition. the high proportion of infants in our study highlights that infants are particularly vulnerable and prone to hospitalization due to severe pneumonia (fancourt et al., 2017; chen et al., 2018; jakhar et al., 2018 ). there was no child known or suspected to be infected with hiv, which is consistent with the very low number of underfive year old children infected with hiv in bhutan (unaids, 2018). abbreviations: crp: c-reactive protein; esr: erythrocyte sedimentation rate; hb: haemoglobin; wbc: white blood cells. a leucocytosis was defined as white blood cells greater than 15 â 10 9 cells/l for children aged between 2 and 11 months and greater than 13 â 10 9 cells/l for children aged between 12 and 59 months. abbreviations: npw: nasopharyngeal washing; pcr: polymerase chain reaction; rsv: respiratory syncytial virus; rt-pcr: real-time polymerase chain reaction. a vials for blood culture were out of stock at the hospital for few weeks during the study period, leading to blood culture not being performed in 12 participants, although molecular screening in bloodspots in filter paper was conducted for all 10 of these children. b coagulase-negative staphylococci, and bacillus spp were considered contaminants, as per our protocol. c bacterial growth was detected in 22 blood cultures, but it was attributed to contamination in 14 cases. d seven children had positive rapid flu test for influenza a, one child for influenza b, and one child for influenza a and b. out of the seven children with rapid flu test positive for influenza a, detection of influenza a by rt-pcr in npw was also positive in four cases, but negative in one case, and "failed/inhibited" in the remaining two cases. for the child with rapid flu test positive for influenza b and for the child with rapid flu test positive for both influenza a and b, rt-pcr in npw was negative for both influenza a and b in both children. e parainfluenza viruses 1, 2, 3, and 4 were detected in 2 (1.7%), 1 (0.9%), 14 (12.2%), and 3 (2.6%) children respectively. f fourteen were influenza a, and two were influenza b. winter, which is the coldest season in bhutan, surprisingly showed the lowest number of cases (10.1%); this finding differs from what is commonly seen in other settings, whereby hospitalization of childhood pneumonia tends to peak during the coldest season (murdoch et al., 2014; ben-shimol et al., 2015) . however, this finding is consistent with those reported by the national sentinel surveillance programme for severe acute respiratory infections, and with the proportion of all-cause paediatric admissions, lower during winter (royal centre for disease control, 2018). this could be partially explained by the fact that winter coincides with the school break in bhutan, with less contact among children; and families moving from the capital to the villages with lower population density. hypoxemia is a well-established predictor of severity in children with pneumonia (duke et al., 2001; lozano, 2001) . a high proportion of children in this study (74.9%) presented with hypoxemia, which is much higher than reported in other settings (subhi et al., 2009; o'brien et al., 2019) . we defined hypoxemia as spo2 < 90%, which is considered appropriate for altitudes under 2500 m, as is the case with thimphu (2334 m). this characteristic might therefore not be generalizable to bhutanese children who live at different altitudes than that of thimphu. while bacterial aetiology was infrequent, viruses were identified in a considerable proportion of children. these microbiological findings coincide more with the etiological profile of pneumonia in children from high-income countries, highlighting the advanced stage of the epidemiologic transition that bhutan seems to have reached (omran, 2005; prayle et al., 2011) . the findings from the perch study, conducted in seven lmics with routine use of pcv, are similar (o'brien et al., 2019) . even in the absence of a deployed pcv in bhutan (pcv was introduced only in january 2019), the burden of pneumococcal invasive disease appears to be low in children. the low proportion of confirmed bacterial cases could be explained by several reasons. first, vaccination coverage was high, which is representative of the rest of the country, although the pcv was not in routine use during the recruitment period (who, 2016) . second, almost one-third of the children had received antibiotics prior to collection of blood sample, which reduces the yield of blood culture by around 45% (berkley et al., 2005; rhodes et al., 2010; driscoll et al., 2017; o'brien et al., 2019) . small blood volume is another factor known to compromise the sensitivity of blood culture (berkley et al., 2005; bouza et al., 2007; driscoll et al., 2017) . blood collection is challenging in children, especially in infants. blood volumes collected for each child were not recorded in this study but, in practice, around 1 ml was dedicated for blood culture in most cases, despite the 2-3 ml recommended in the protocol. nevertheless, these findings confirm the low yield of blood culture in hospitalized children with pneumonia and question both the need of blood culture for uncomplicated cases of pneumonia and using blood culture as the preferred screening tool for invasive bacterial disease in children with pneumonia. molecular methods have been found to be more sensitive than blood culture to detect pneumococcal invasive disease (muñozalmagro et al., 2011; selva et al., 2013; o'brien et al., 2019) . this was not the case in this study. b. pertussis was isolated in respiratory samples of three children. this is similar to the detection rate of around 1% of hospitalized pneumonia cases in similar studies (jroundi et al., 2014; barger-kamate et al., 2016) . one of these three children, aged five months, had a fatal outcome. this underlines the high fatality ratio of pertussis-infected pneumonia, especially in infants who are unvaccinated, and suggests the need of intervention such as maternal vaccination to reduce morbi-mortality associated with pertussis in vulnerable populations. viral detection was common. the use of pcr techniques has increased the ability to detect respiratory viruses (ruuskanen et al., 2011) . however, evidence of the detection of viruses in asymptomatic individuals has raised concern about the clinical significance of these positive findings. attribution of causality is not straightforward, as viruses can commonly be found both in symptomatic but also asymptomatic individuals (jartti et al., 2008; ruuskanen et al., 2011; rudan et al., 2013; o'brien et al., 2019) . while the causative role of rsv, influenza, adenovirus, human metapneumovirus, and bocavirus in childhood pneumonia is wellestablished, the pathogenic role of other viruses such as rhinovirus is still questioned (fry et al., 2007; caracciolo et al., 2008; ruuskanen et al., 2011; shi et al., 2017; jayaweera et al., 2018; o'brien et al., 2019) . using molecular methods, rhinovirus has been shown to be the most frequent respiratory pathogen isolated in children, and its detection in asymptomatic children is significantly higher than other respiratory viruses (kusel et al., 2006; jartti et al., 2008; ruuskanen et al., 2011) . nevertheless, clinical relevance of rhinovirus has been proven by the association of this virus with respiratory symptoms in children, mainly wheezing (kusel et al., 2006; khetsuriani et al., 2007) . in our series, 27.5% of the children with rhinovirus presented with wheezing. infection with coronavirus (cor229e, corhku1, cornl63, coroc43) was low in the present study. similarly, the new coronavirus (sars-cov-2) seems to cause a low infection rate in children (world health organization, 2020). the reason why coronavirus infection rate in children is low is unknown. in addition, the interpretation of positive viral findings is challenging due to the identification of multiple co-existing viral infections (jartti et al., 2008; ruuskanen et al., 2011) . co-infections were common in the present study, which is consistent with the existing literature (ruuskanen et al., 2011; jroundi et al., 2014; jiang et al., 2017) . considering radiological pneumonia endpoint as a proxy for bacterial pneumonia, 27.0% of children with positive npw findings had a viral-bacterial co-infection, and 40.0% of children with influenza detected in npw had an influenzabacterial co-infection. the contribution of viral-bacterial coinfections is well-acknowledged in the aetiology of childhood pneumonia, particularly the interaction between influenza virus and s. pneumoniae (o'brien et al., 2000; kwofie et al., 2012; brealey et al., 2015) . the combined effect of bacteria and viruses was shown to increase the severity of the disease, and bidirectional interactions have been described: respiratory viruses leading to bacterial superinfection, and bacteria pathogens promoting respiratory viral superinfections (brealey et al., 2015) . however, there is still a lack of robustness supporting these findings. this study has several limitations. most children in the present study lived in thimphu, and the microbiological findings may not be generalized to the rest of the country. bhutan is very diverse: comprised of cities, such as thimphu, and isolated households in very remote areas, leading to different lifestyles and environmental exposures; and also diverse in terms of altitude, with different climates and precipitations. the burden of pneumonia requiring hospitalization was highest among infants. respiratory viruses were detected in a considerable number of children, although a clear pathogenic role cannot be established. together with the relatively low proportion of children presenting a likely bacterial pneumoniaaround a quarter as per positive blood culture and radiological findingsthese findings emphasize the advanced stage of the epidemiologic transition that bhutan seems to have reached. this study is the first step to better understand the aetiology and clinicopathological characteristics of pneumonia in bhutanese children. henceforth, the development of targeted pneumonia interventions and hypothesis-driven research is encouraged to reduce the morbidity and mortality associated with this disease. fostering a robust pneumonia aetiology surveillance in children under five years of age appears important and would allow the assessment of the impact of the recently introduced pcv in reducing the burden of pneumonia. funding sj received a pre-doctoral fellowship from the secretariat of universities and research, ministry of enterprise and knowledge of the government of catalonia and co-funded by european social fund. this work was supported by a scholarship from the spanish society of paediatric infectology (sociedad española de infectología pediátrica, seip). none of the funding sources were involved in the study design, data collection, analysis, interpretation of the data, and writing of the manuscript. the study protocol was approved by the research ethics board of health, ministry of health, in thimphu in march 2017 (protocol number po/2016/086), and by the research ethics committee from the hospital clínic in barcelona (hcb/2017/0741). pertussis-associated pneumonia in infants and children from low-and middleincome countries participating in the perch study seasonality of both bacteremic and nonbacteremic pneumonia coincides with viral lower respiratory tract infections in early childhood, in contrast to nonpneumonia invasive pneumococcal disease, in the pre-pneumococcal conjugate vaccine era severity of pneumonia in under 5-year-old children from developing countries: a multicenter, prospective, observational study bacteremia among children admitted to a rural hospital in kenya is the volume of blood 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role of preceding influenza infection the epidemiologic transition: a theory of the epidemiology of population change pneumonia in the developed world clinical features for diagnosis of pneumonia in children younger than 5 years: a systematic review and meta-analysis antibiotic use in thailand: quantifying impact on blood culture yield and estimates of pneumococcal bacteremia incidence epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries viral pneumonia systematic review of the diagnostic accuracy of c-reactive protein to detect bacterial infection in nonhospitalized infants and children detection of streptococcus pneumoniae and haemophilus influenzae type b by real-time pcr from dried blood spot samples among children with pneumonia: a useful approach for developing countries global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study usa: college station the prevalence of hypoxaemia among ill children in developing countries: a systematic review world bank country and lending groups united nations interagency group for child mortality estimation country fact sheets bhutan sustainable development goals global burden of childhood pneumonia and diarrhoea world health organization. revised who classification and treatment of childhood pneumonia at health facilities. geneva: evidence summaries world health organization. the kingdom of bhutan health system review world health organization. coronavirus disease (covid-19) outbreak we thank all the children and their parents or caregivers who participated in this study, as well as the paediatric department of jdwnrh including paediatricians, residents in paediatrics, and interns who contributed to identifying eligible cases for the study. we are very grateful to all nurses who participated in the collection of biological samples and contributed to the success of this study, especially those in the paediatric ward. we thank dr. kinley tshering, paediatrician, who read and interpreted all the chest radiographies; the radiological and microbiological departments of jdwnrh for their support; and laia blanco lopez for contributing to the microbiological analysis of viruses in npw. we are very grateful to gaurav kwatra and laura puyol for their assistance in the shipment of the biological samples.we are grateful to the spanish society of paediatric infectology (sociedad española de infectología pediátrica, seip) for their financial support, which contributed to the shipment and testing of biological samples. we acknowledge support from the spanish ministry of science and innovation through the "centro de excelencia severo ochoa 2019-2023" program (cex2018-000806-s), and support from the generalitat de catalunya through the cerca program. cism is supported by the government of mozambique and the spanish agency for international development (aecid). no conflict of interest to declare. supplementary material related to this article can be found, in the online version, at https://doi.org/10.1016/j.ijid.2020.04.017. key: cord-326143-6ndqgxy8 authors: wang, qiang; hu, zhao title: successful recovery of severe covid-19 with cytokine storm treating with extracorporeal blood purification date: 2020-05-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.065 sha: doc_id: 326143 cord_uid: 6ndqgxy8 covid-19 associated cytokine storm could induce ards rapidly and the patients would require the support of mechanic ventilation. however, the prognosis was not that optimistic. the outcome might be changed if the intervention of ebp was performed timely. we present a case of severe sars-cov-2 infection who recovered from cytokine storm. the coronavirus disease 2019 (covid-19) broke out throughout the world now. the total number of deaths has been over 88900 up to now. the patients with confirmed covid-19 progressed to acute respiratory distress syndrome (ards) rapidly in an incident rate as high as 41.8% 1 , and many of them require mechanic ventilation. in a cohort of an intensive care unit (icu) from italy, 1287 cases need respiratory support, and among them, 88% of patients (1150 cases) had to be supported with mechanical ventilation 2 . apart from the desperate lacking of ventilator all over the world, mechanical ventilation could also cause barotrauma and ventilator-associated lung injury. cytokine storm has been disclosed as the main pathological characteristic of covid-19 3 , and it is also the direct pathogenic contributor to induce ards. cytokines could be eliminated effectively by extracorporeal blood purification (ebp) 4 , which thus could interrupt the initiation and progression of inflammation cascade in the scenario of covid-19. accordingly, there may be a chance of avoiding incubation and mechanical ventilation. herein, we report a case of severe sars-cov-2 infection with cytokine storm, who was completely recovered from cytokine storm using extracorporeal blood purification. a 62-year-old male presented to the hospital with 8-day history of fever and 6-day history of cough and chest distress. the patient had a history of gallstone. he got fever on day 1 (february 14, 2020) and had chill, headache, muscle soreness, fatigue, nausea, cough, and chest distress and shortness of breath on day 3. then, he was quarantined in a hotel. being tested positive j o u r n a l p r e -p r o o f for sars-cov-2 on day 5, he received oseltamivir, moxifloxacin and lianhua qingwen capsule (chinese medicine) in the outpatient. he was admitted to the hospital with fever, cough and mild chest distress on day 9. arbidol, hydroxychloroquine, oseltamivir, and lianhua qingwen capsule were administered. supplemental oxygen was delivered by nasal cannula at 2 l/min. alterations in hepatic function were showed: levels of alanine aminotransferase (81 u/l, normal range: 9-50 u/l) and aspartate aminotransferase (94 u/l, normal range: 15-40 u/l) were elevated, and cd3 and cd4 cell counts were markedly decreased (supplemental table) on day 10. chest ct indicated multiple ground-glass opacities in bilateral lungs on day 11 (supplemental figure 1 . a-c). the peak of temperature was 38.5°c up to date. his vital signs remained clinically stable except oxygen saturation was 97% while providing oxygen at 3 l/min. il-6 (198.66 pg/ml) was almost 10 folds of normal range (≤5.9 pg/ml) which indicated an initiation of cytokine storm on day 12 ( figure 1 ). the ebp, including double plasma molecular adsorption system (bs330 and ha330ii, jafron, china) and plasma exchange (2000 ml each), was thus applied to remove the cytokines on day 13. the bs330 and ha330ii were installed in series after the plasma separator (ec-4w, asahi) with a blood flow velocity of 80-100 ml/min and a separating speed of 20-25ml/min, and the duration of the treatments was 6 hours. the plasma exchange was then conducted. intravenous methylprednisolone (40 mg daily) was used to suppress the inflammation reaction. the patient was largely stable until the chest distress exacerbated and blood in phlegm developed on day 14. he then progressed to type i respiratory failure (partial pressure of oxygen 51 mmhg, partial pressure of carbon dioxide 32 mmhg) with 89% oxygen saturation while the oxygen flow was 3 l/min. high-flow oxygen (40 l/min) was initiated to keep the oxygen saturation values between 96-99%. hydroxychloroquine was discontinued due to a long qt interval. the ebp therapy continued on days 14 and 15 respectively. the patient was transferred into icu on day 15. given the acute inflammatory reaction, methylprednisolone was improved to 60 mg twice daily, and piperacillin-tazobactam (4.5 g administered intravenously every 8 hours) was initiated concerning about the hospital-acquired pneumonia. acetylcysteine was used to dilute the phlegm. the human serum albumin and other supportive care were also administered. the clinical condition of the patient was improved on day 16 and was stable j o u r n a l p r e -p r o o f thereafter, and his hepatic function was back to normal as well. the body temperature returned to normal on day 17. the igm of anti-sars-cov-2 was identified (77.11 au/ml, normal value <10 au/ml) at the same day. methylprednisolone was gradually reduced and discontinued on day 23. the lesions on chest ct was confined on day 17 and further alleviated on day 21 and almost disappeared on day 33 (supplemental figure 1) . low flow rate of oxygen (2 l/min) was delivered instead of high-flow oxygen on day 26 then discontinued on day 36. he was asymptomatic at rest and had no shortness of breath while doing activity training. his renal function was unaffected and immunoglobulin levels including igg, igm, iga and ige were normal throughout the clinical course. complement c3 level was staying below the normal range (0.9-1.8 g/l) during the hospital duration (supplemental table 1 ). c4 level (<0.06 g/l, normal range: 0.1-0.4 g/l) was reduced at day 16 and was back to normal (0.15 g/l) on day 31. the nucleic acid testing of sars-cov-2 was negative in four different times. he was discharged on day 38. the management of covid-19 in critical cases is still challenging nowadays. respiratory and circulation supports, such as mechanic ventilation and extracorporeal membrane oxygenation (ecmo), were almost the last defense for severe covid-19 5 . although specific methods to intervene the progression of critical cases are unknown, the effects of ebp in treatment of covid-19 associated cytokine storm have not been emphasized. the outcome of the present case of covid-19 with ards is promising. pulmonary fibrosis was not observed up to date. ebp was suggested to interrupt the inflammation cascade and stop the progression of cytokine storm in this case. there were obvious peak levels of cytokines and bent over after the initiation of ebp on day 13. ha330 improved oxygenation and lung mechanics by removing circulating and alveolar cytokine levels 6 , and bs330 adsorbed bilirubin so as to attenuate liver injury 7 .the ebp that combined the double plasma molecular adsorption system and plasma exchange can directly reduce the cytokines. although methylprednisolone was also administered synchronously, it has been identified that the significant time point of il-6 reduce was the seventh day rather than the first three days in ards 8 risk factors associated with acute respiratory distress syndrome and death in patients with coronavirus disease baseline characteristics and outcomes of 1591 patients infected with sars-cov-2 admitted to icus of the lombardy region clinical features of patients infected with 2019 novel coronavirus in wuhan cytokine removal in human septic shock: where are we and where are we going? ann intensive care initial elso guidance document: ecmo for covid-19 patients with severe cardiopulmonary failure hemoadsorption therapy in the critically ill: solid base but clinical haze preparation and adsorption properties of novel porous microspheres with different concentrations of bilirubin effect of methylprednisolone on inflammatory markers and patients' outcomes in acute respiratory distress syndrome clinical characteristics of coronavirus disease 2019 in china clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan key: cord-336954-rh88lod0 authors: shim, eunha; tariq, amna; choi, wongyeong; lee, yiseul; chowell, gerardo title: transmission potential and severity of covid-19 in south korea date: 2020-03-18 journal: int j infect dis doi: 10.1016/j.ijid.2020.03.031 sha: doc_id: 336954 cord_uid: rh88lod0 objectives: since the first case of 2019 novel coronavirus (covid-19) identified on jan 20, 2020 in south korea, the number of cases rapidly increased, resulting in 6,284 cases including 42 deaths as of march 6, 2020. to examine the growth rate of the outbreak, we aimed to present the first study to report the reproduction number of covid-19 in south korea. methods: the daily confirmed cases of covid-19 in south korea were extracted from publicly available sources. by using the empirical reporting delay distribution and simulating the generalized growth model, we estimated the effective reproduction number based on the discretized probability distribution of the generation interval. results: we identified four major clusters and estimated the reproduction number at 1.5 (95% ci: 1.4-1.6). in addition, the intrinsic growth rate was estimated at 0.6 (95% ci: 0.6, 0.7) and the scaling of growth parameter was estimated at 0.8 (95% ci: 0.7, 0.8), indicating sub-exponential growth dynamics of covid-19. the crude case fatality rate is higher among males (1.1%) compared to females (0.4%) and increases with older age. conclusions: our results indicate early sustained transmission of covid-19 in south korea and support the implementation of social distancing measures to rapidly control the outbreak. a novel coronavirus (sars-cov-2) that emerged out of the city of wuhan, china in december 2019 has already demonstrated its potential to generate explosive outbreaks in confined settings and cross borders following human mobility patterns (mizumoto et al., 2020) . while covid-19 frequently induces mild symptoms common to other respiratory infections, it has also exhibited an ability to generate severe disease among certain groups including older populations and individuals with underlying health issues such as cardiovascular disease and diabetes (adler, 2020) . nevertheless, a clear picture of the epidemiology of this novel coronavirus is still being elucidated. the number of cases of covid-19 in the province of hubei, the disease epicenter, quickly climbed following an exponential growth trend. the total number of covid-19 cases is at 80,859 including 3,100 deaths in china as of march 8, 2020 (who, 2020 . fortunately, by february 15, 2020 the daily number of new reported cases in china started to decline across the country although hubei province reported 128 cases on average per day in the week of march 2-8, 2020 (who, 2020) . while the epidemic continues to decline in china, 24,727 covid-19 cases have been reported in more than 100 countries outside of china including south korea, italy, iran, japan, germany, and france (who, 2020). in particular, south korea quickly became one of the hardest hit countries with covid-19, exhibiting a steadily increasing number of cases over the last few days. hence, it is crucial to monitor the progression of these outbreaks and assess the effects of various public health measures including the social distancing measures in real time. the first case in south korea was identified on january 20, 2020 followed by the detection of one or two cases on average in the subsequent days. however, the number of confirmed cases of sars-cov-2 infection started to increase rapidly on february 19, 2020 with a total of 6,284 confirmed covid-19 cases including 42 deaths reported as of march 6, 2020 according to the korea centers for disease control and prevention (kcdc) (kcdc, 2020) ( table 1 ). the epicenter of the south korean covid-19 outbreak has been identified in daegu, a city of 2.5 million people, approximately 150 miles south east of seoul. the rapid spread of covid-19 in south korea has been attributed to one case linked to a superspreading event that has led to more than 3,900 secondary cases stemming from church services in the city of daegu (kuhn, 2020 , ryall, 2020 . this has led to sustained transmission chains of covid-j o u r n a l p r e -p r o o f 19, with 55% of the cases associated with the church cluster in daegu (bostock, 2020) . moreover, three other clusters have been reported including one set in chundo daenam hospital in chungdo-gun, gyeongsanggbuk-do (118 cases), one set in the gym in cheonan, chungcheongnam-do (92 cases), and one pilgrimage to israel cluster in gyeongsanggbuk-do (49 cases). these few clusters have become the major driving force of the infection. a total of 33 cases were imported while the four major clusters are composed of local cases as described in table 2 . transmission of sars-cov-2 in korea has been exacerbated by amplified transmission in confined settings including a hospital and a church in the city of daegu. the hospital-based outbreak alone involves 118 individuals including 9 hospital staff (news, 2020) , which is reminiscent of past outbreaks of sars and mers (chowell et al., 2015) . to respond to the mounting number of cases of covid-19, the korean government has raised the covid-19 alert level to the highest (level 4) on february 23, 2020 to facilitate the implementation of comprehensive social distancing measures including enhanced infection control measures in hospitals, restricting public transportation, cancelling social events, and delaying the start of school activities (kim, 2020) . while the basic reproduction number, denoted by r0, applies at the outset of an exponentially growing epidemic in the context of an entirely susceptible population and in the absence of public health measures and behavior changes, the effective reproduction number (rt) quantifies the time-dependent transmission potential. this key epidemiological parameter tracks the average number of secondary cases generated per case as the outbreak progresses over time. steady values of rt above 1 indicate sustained disease transmission, whereas values of rt <1 do not support sustained transmission and the number of new cases is expected to follow a declining trend. in this report, using a mathematical model parameterized with cases series of the covid-19 outbreak in korea, we investigate the transmission potential and severity of covid-19 in korea using early data of local and imported cases reported up until february 26, 2020. we obtained the daily series of confirmed cases of covid-19 in south korea from january 20, 2020 to february 26, 2020 that are publicly available from the korea centers for disease control and prevention (kcdc) (kcdc, 2020). our data includes the dates of reporting for all confirmed cases, the dates of symptom onsets for the first 28 reported cases, and whether the case is autochthonous (local transmission) or imported. we also summarize the case clusters comprising one or more cases according to the source of infection according to the field investigations conducted by the kcdc (kcdc, 2020). accordingly, four major clusters were identified. the total number of confirmed and suspected cases as of march 6, 2020 as well as the crude case and fatality rate distribution by gender and age are presented in table 1 . to estimate the growth rate of the epidemic, it is ideal to characterize the epidemic curve according to dates of symptoms onset rather than according to dates of reporting. for the covid-19 data in korea, the symptom onset dates are available for only the first 28 reported cases. moreover, all of the dates of symptoms onset are available for the imported cases. therefore, we utilize this empirical distribution of reporting delays from the onset to diagnosis to impute the missing dates of onset for the remainder of the cases with missing data. for this purpose, we reconstruct 300 epidemic curves by dates of symptoms onset from which we derive a mean incidence curve of local case incidence and drop the last three data points from the analysis to adjust for reporting delays in our real-time analysis (tariq et al., 2019) . we assess the effective reproduction number, , which quantifies the time dependent variations in the average number of secondary cases generated per case during the course of an outbreak due to intrinsic factors (decline in susceptible individuals) and extrinsic factors (behavior changes, cultural factors, and the implementation of public health measures) (anderson and may, 1991 , chowell et al., 2015 . using the korean incidence curves for imported and local cases, we estimate the evolution of rt for covid-19 in korea. first, we characterize daily local case incidence using the generalized growth model (ggm) (viboud et al., 2016) . this model characterizes the growth profile via two parameters: the growth rate parameter ( ) and the scaling of the growth rate parameter ( ). the model captures diverse epidemic profiles ranging from constant incidence ( = 0 ), sub-exponential or polynomial growth (0 < < 1), and exponential growth ( = 1) (viboud et al., 2016) . the generation interval is assumed to follow a gamma distribution with a mean of 4.41 days and a standard deviation of 3.17 days (nishiura et al., 2020 , you et al., 2020 . next, to estimate the most recent estimate of rt, we simulate the progression of incident cases from ggm, and apply the discretized probability distribution ( ) of the generation interval using the renewal equation (h. nishiura, 2009 , nishiura and chowell, 2014 , paine et al., 2010 given by in the renewal equation we denote the local incidence at calendar time by , and the raw incidence j o u r n a l p r e -p r o o f of imported cases at calendar time by . the parameter 0 ≤ ≤ 1 quantifies the relative contribution of imported cases to the secondary disease transmission (nishiura and roberts, 2010) . the denominator represents the total number of cases that contribute to the incidence cases at time . next, we estimate for 300 simulated curves assuming a poisson error structure to derive the uncertainty bounds around the curve of (chowell, 2017) . the reconstructed daily incidence curve of covid-19 after the imputing the onset dates for the korean cases is shown in figure 1 . between january 20 and february 18, 2020 an average of 2 new cases were reported each day, whereas between february 19-26, 2020, 154 new cases were reported on average each day. under the empirical reporting delay distribution from early korean cases with available dates of onset, the intrinsic growth rate (r) was estimated at 0.6 (95% ci: 0.6, 0.7) and the scaling of growth parameter (p) was estimated at 0.8 (95% ci: 0.7, 0.8), indicating sub-exponential growth dynamics of covid-19 in korea (figure 2 , table 3 ). the mean reproduction number was estimated at 1.5 (95% ci: 1.4, 1.6) as of february 26, 2020. our estimates of are not sensitive to the changes to the parameter that modulates the contribution of the imported cases to transmission ( ). the crude case fatality rate is higher among males (1.1%) compared to females (0.4%) and increases with older age, from 0.1% among those 30-39 yrs to 6% among those >=80 yrs as of march 6, 2020. spatial distribution of the korean clusters is shown in figure 3 and the characteristics of each cluster are presented in table 2 as of march 8, 2020. as in the central cities of cheonan, 92 covid-19 patients were associated with to a zumba dance class after an instructor became the 5th confirmer of cheonan on february 25, 2020. according to the provincial government of south chungcheong province, everyone who attended the class in cheonan was tested, and 27 cases were confirmed on february 28, 2020, with most of the cases being women in their 30's and 40's (kcdc, 2020). as of march 8, 2020, a total of 92 individuals were infected including zumba instructors and students as well as their families and acquaintances (kcdc, 2020) . this cluster is comprised of 49 cases as of march 8, 2020. this cluster was identified when 31 catholic pilgrims visited israel between february 8, 2020 and february 16, 2020 and were subsequently confirmed for covid-19 (2020). amongst these, 11 individuals were diagnosed on february 17, 2020, while 20 others were confirmed positive between february 21-25, 2020 and quarantined immediately. of the 31 infected pilgrims, 19 belong to the euiseong county, north gyeongsang province, while one patient, a tour guide belongs to seoul. health authorities have traced multiple contacts from the cases of this cluster, and additional cases were confirmed thereafter, raising concerns about the potential risk of secondary infections. this is the first study to report estimates of the transmission potential of covid-19 in korea based on j o u r n a l p r e -p r o o f the trajectory of the epidemic, which was reconstructed by using the dates of onset of the first reported cases in korea. the estimates of r clearly indicate sustained transmission of the novel coronavirus in korea and the case fatality rate appears to be higher among males and older populations (table 1) . moreover, the imported cases contribute little to the secondary disease transmission in korea, as majority of these cases occurred in the early phase of the epidemic, with the most recent imported case reported on february 9, 2020. these findings support the range of social distancing interventions that the korean government put in place in order to bring the outbreak under control as soon as possible. our estimates of the reproduction number can be compared with earlier estimates reported for the epidemic in china where the estimates of r lie in the range 2-7.1 (lai et al., 2020 , li et al., 2020 , mizumoto et al., 2020 , read et al., 2020 group for control of the epidemic of novel coronavirus pneumonia of the chinese preventive medicine, 2020, wu et al., 2020 , zhang et al., 2020 . moreover, the mean r reached values as high as ~11 for the outbreak that unfolded aboard the princess cruises ship during january-february 2020 (mizumoto and chowell, 2020) . in contrast, a recent study on singapore's covid-19 transmission dynamics reported lower estimates for (1.1, 95% ci: 1.1, 1.3) as of february 19 th , 2020, reflecting a significant impact of the control interventions that have been implemented in singapore (tariq et al., 2020) . the estimates of the scaling of growth parameter (p) in our study indicate sub-exponential growth dynamics of covid-19 in korea. this aligns well with the sub-exponential growth patterns of covid-19 in singapore and all chinese provinces except hubei , tariq et al., 2020 . since the first covid-19 case was reported on january 20, 2020, the epidemic's trajectory showed a rapid upturn until february 18, 2020, when a super spreader (case 31) was identified in the shincheonji (cowling et al., 2015) . amplification of mers in the hospital setting has been associated with diagnostic delays, which increase the window of opportunity for the generation of secondary cases (chowell et al., 2015) . this underscores the need for rapid testing, case detection and active contact tracing to isolate infectious individuals. beyond korea, substantial covid-19 transmission has been reported in italy, iran, germany, france, and aboard the diamond cruise ship (marcus, 2020 , woods, 2020 contributions: es, at and gc analyzed the data. ys and wc retrieved and managed the data. es, at, and gc wrote the first draft of the paper. all authors contributed to the writing of the paper. korean pilgrims to israel infected with coronavirus: authorities. yonhap news seoul why coronaviruses hit older adults hardest infectious diseases of south korea is testing 200,000 members of a doomsday church linked to more than 60% of its coronavirus cases. business insider fitting dynamic models to epidemic outbreaks with quantified uncertainty: a primer for parameter uncertainty, identifiability, and forecasts transmission characteristics of mers and sars in the healthcare setting: a comparative study preliminary epidemiological assessment of mers-cov outbreak in south korea the effective reproduction number as a prelude to statistical estimation of time-dependent epidemic trends the updates on covid-19 in korea as of 25 february as covid-19 cases rise, south korea raises virus threat level to its maximum secretive church sect at the center of south korea's coronavirus 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and importations. euro surveillance : bulletin europeen sur les maladies transmissibles novel coronavirus 2019-ncov: early estimation of epidemiological parameters and epidemic predictions real-time forecasts of the covid-19 epidemic in china from surge in south korea virus cases linked to church 'super-spreader'. the telegraph: telegraph media group limited special expert group for control of the epidemic of novel coronavirus pneumonia of the chinese preventive medicine a real-time monitoring the transmission potential of covid-19 in singapore assessing reporting delays and the effective reproduction number: the ebola epidemic in drc a generalized-growth model to characterize the early ascending phase of infectious disease outbreaks 44 new coronavirus cases reported on quarantined diamond princess cruise nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study. the lancet 2020 estimation of the reproductive number of novel coronavirus (covid-19) and the probable outbreak size on the diamond princess cruise ship: a datadriven analysis preliminary prediction of the basic reproduction number of the wuhan novel coronavirus 2019-ncov growth rate, r 0.6 (95% ci:0.6,0.7)scaling of growth parameter, p 0.8 (95% ci:0.7,0.8) key: cord-257737-obadq502 authors: wu, di; lu, jianyun; liu, yanhui; zhang, zhoubin; luo, lei title: positive effects of covid-19 control measures on influenza prevention date: 2020-04-10 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.009 sha: doc_id: 257737 cord_uid: obadq502 abstract coronavirus disease 2019 (covid-19) caused by severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has now become a pandemic threat to the whole world. at the same time, influenza virus has been active, with influenza virus and sars-cov-2 sharing the same transmission routes. this article aims to alert clinicians of the presence of co-infection with these two viruses and to describe the effect of the measures taken to fight covid-19 on influenza prevention and control. j o u r n a l p r e -p r o o f al. [ 4 ] have reported the case of a patient co-infected with sars-cov-2 and influenza a virus. also, li and wang [ 5 ] have reported the need to be alert to the superposed effect of seasonal influenza while fighting pneumonia caused by the novel coronavirus. according to the chinese national influenza center, ili activity (ili%) in 2020 in south china was lower than that in north china from week 5 to week 10, and this situation reversed in the subsequent 2 weeks; in contrast, in 2019, ili% was constantly higher in south china than in north china for the first 11 weeks (except for the first week of 2019) ( figure 1a ) [au?1]. overall, ili% in 2020 across the whole of china has been higher than that observed in 2019, and the same trend has been observed in the positive rate of specimens ( figure 1b ). [ figure 1 here] guangzhou city, in south china, has also seen a relatively higher ili% over summary of a report of 72 314 cases from the chinese center for disease control and prevention who. coronavirus disease 2019 (covid-19) situation report -71 influenza update -362, based on data up to 16 co-infection with sars-cov-2 and influenza a virus in patient with pneumonia be alert to superposed effect of seasonal influenza while fighting against novel coronavirus pneumonia key: cord-297829-aynigoud authors: zhang, li; seale, holly; wu, shuangsheng; yang, peng; zheng, yang; ma, chunna; macintyre, raina; wang, quanyi title: post-pandemic assessment of public knowledge, behavior, and skill on influenza prevention among the general population of beijing, china date: 2014-04-13 journal: int j infect dis doi: 10.1016/j.ijid.2014.01.003 sha: doc_id: 297829 cord_uid: aynigoud background: the aim of this study was to assess the knowledge, behavioral, and skill responses toward influenza in the general population of beijing after pandemic influenza a (h1n1) 2009. methods: a cross-sectional study was conducted in beijing, china, in january 2011. a survey was conducted in which information was collected using a standardized questionnaire. a comprehensive evaluation index system of health literacy related to influenza was built to evaluate the level of health literacy regarding influenza prevention and control among residents in beijing. results: thirteen thousand and fifty-three valid questionnaires were received. the average score for the sum of knowledge, behavior, and skill was 14.12 ± 3.22, and the mean scores for knowledge, behavior, and skill were 4.65 ± 1.20, 7.25 ± 1.94, and 2.21 ± 1.31, respectively. the qualified proportions of these three sections were 23.7%, 11.9%, and 43.4%, respectively, and the total proportion with a qualified level was 6.7%. there were significant differences in health literacy level related to influenza among the different gender, age, educational level, occupational status, and location groups (p < 0.05). there was a significant association between knowledge and behavior (r = 0.084, p < 0.001), and knowledge and skill (r = 0.102, p < 0.001). conclusions: the health literacy level remains low among the general population in beijing and the extent of relativities in knowledge, behavior, and skill about influenza was found to be weak. therefore, improvements are needed in terms of certain aspects, particularly for the elderly and the population of rural districts. educational level, as a significant factor in reducing the spread of influenza, should be considered seriously when intervention strategies are implemented. pandemic influenza a (h1n1) 2009, a new strain of triplereassortant influenza a virus composed of a combination of human, swine, and eurasian avian strains, spread rapidly through more than 200 countries 1 and was the first global pandemic of the 21st century. 2,3 on august 10, 2010 the world health organization (who) declared that we had entered the post-pandemic period and the h1n1 virus had taken on the behavior of a seasonal influenza virus. 4 there was an effective control and prevention campaign during and after the 2009 influenza pandemic in beijing, which included identifying, treating, and isolating people who had the disease and educating the public about the steps that individuals could take to reduce the risk of transmission. meanwhile, health education campaigns touching on good hygiene practices and social distancing were implemented in hospitals, schools, local communities, and through mass media. 5 since the severe acute respiratory syndrome (sars) outbreak in 2003, the government of china has strengthened its surveillance and established the prevention and control system for infectious disease. 6 the level of science and technology in this field in china has since improved significantly. compared with the abundant research on how the government and institutions could improve the surveillance management and prevention system, there have been few public reports assessing the effect of these policies and the level of health literacy associated with influenza prevention in the general population. background: the aim of this study was to assess the knowledge, behavioral, and skill responses toward influenza in the general population of beijing after pandemic influenza a (h1n1) 2009. methods: a cross-sectional study was conducted in beijing, china, in january 2011. a survey was conducted in which information was collected using a standardized questionnaire. a comprehensive evaluation index system of health literacy related to influenza was built to evaluate the level of health literacy regarding influenza prevention and control among residents in beijing. results: thirteen thousand and fifty-three valid questionnaires were received. the average score for the sum of knowledge, behavior, and skill was 14.12 ae 3.22, and the mean scores for knowledge, behavior, and skill were 4.65 ae 1.20, 7.25 ae 1.94, and 2.21 ae 1.31, respectively. the qualified proportions of these three sections were 23.7%, 11.9%, and 43.4%, respectively, and the total proportion with a qualified level was 6.7%. there were significant differences in health literacy level related to influenza among the different gender, age, educational level, occupational status, and location groups (p < 0.05). there was a significant association between knowledge and behavior (r = 0.084, p < 0.001), and knowledge and skill (r = 0.102, p < 0.001). conclusions: the health literacy level remains low among the general population in beijing and the extent of relativities in knowledge, behavior, and skill about influenza was found to be weak. therefore, improvements are needed in terms of certain aspects, particularly for the elderly and the population of rural districts. educational level, as a significant factor in reducing the spread of influenza, should be considered seriously when intervention strategies are implemented. ß 2014 the authors. published by elsevier ltd on behalf of international society for infectious diseases. it has been shown that health education is directed towards improving health literacy 7 and it is expected that this would have a positive effect on influenza prevention and control in the future. there has been no investigation regarding health literacy of influenza prevention in the general population of beijing. after the 2009 pandemic, it was necessary to collect some baseline data to understand and monitor public perceptions and behaviors. we conducted a survey in six districts of beijing, china, in early 2011 to assess the influenza-related health literacy level in the general population of beijing after the 2009 influenza pandemic, and to explore the behavior and skill factors affecting the incidence level of influenza. a cross-sectional study was conducted in beijing, china, in january 2011. subjects were recruited via a multi-stage stratified cluster sampling technique. first, three urban districts and three rural districts were selected randomly from a total of 18 districts in beijing. five sub-districts/towns were then selected randomly in each of the six districts, from which five communities were selected randomly. lastly, 18 subjects for each age group (18-29, 30-39, 40-49, 50-59, and !60 years) were recruited from each community, with equal weighting of the sexes. the standardized interview questionnaire was designed to collect the following data: (1) socio-demographic characteristics (gender, age, education, occupation, and general health status); (2) knowledge about the disease and its symptoms; (3) practices towards influenza and people with influenza-like-illness (i.e., avoidance practices, cough etiquette, use of masks, hand washing, being vaccinated, health-seeking behaviors); (4) perceived ability to avoid illness; (5) attitudes towards the vaccine, and (6) comprehension of health materials related to influenza (i.e., medication instructions, educational information about influenza and the vaccine). lastly, participants were asked to gauge their ability to use a thermometer. questions were divided into three sections under the headings of knowledge, behaviors, and skills. after obtaining informed consent from the subject, the survey was administered by face-to-face interview. for the purpose of analysis, each question that was answered positively was given a score of 1 and each question that was answered negatively or was answered as 'don't know' was given a score of 0. the total score for the three sections was 24 points: the total score for 'knowledge' was 7 points, and a qualified level was considered to be 6-7 points; the total score for 'behavior' was 13 points, and a qualified level was considered to be 10-13 points; the total score for 'skill' was 4 points, and a qualified level was considered to be 3-4 points. questionnaire data were entered in duplicate using epidata software, and data were analyzed using spss 18 statistical software (spss inc., chicago, il, usa). descriptive statistics, such as percentages, means, and standard deviations, were calculated. to analyze the significance of the continuous data, an analysis of variance (anova) was applied. chi-square tests of significance were used for analyses of categorical variables regarding the qualified proportion of the three sections. the relationships among knowledge, behavior, and skill were analyzed by correlation analysis. statistical significance was accepted at p < 0.05 for all analyses. this study was approved by the institutional review board and human research ethics committee of the beijing center for disease prevention and control (cdc). a total of 13 286 adults were approached; 13 053 valid questionnaires were received, giving an effective response rate was 98.1%. the demographic characteristics of participants are reported in table 1 . the average score for the sum of knowledge, behavior, and skill was 14.12 ae 3.22, and the mean scores for knowledge, behavior, and skill were 4.65 ae 1.20, 7.25 ae 1.94, and 2.21 ae 1.31, respectively. the statistic of the total score of these three sections was found to follow an approximately normal distribution. the overall mean score for knowledge was 4.65 ae 1.20, and 23.7% of participants met the qualified standard of knowledge. both the overall knowledge score and the qualified proportion for knowledge were significantly higher in urban areas compared to rural areas (f = 63.968, p < 0.001; chi-square = 12.701, p < 0.001). the mean knowledge score fell significantly with increasing age (f = 31.064, p < 0.001) and increased significantly with higher educational levels (f = 158.175, p < 0.001) ( table 2 ). the qualified proportion in the different age groups fell significantly with increasing age (chi-square = 20.991, p < 0.001) and increased significantly with higher educational levels (chi-square = 92.145, p < 0.001) ( table 3) . males had a significantly higher mean score for behavior than females (f = 92.904, p < 0.001). the mean score of urban residents was significantly higher than that of rural residents (f = 54.786, p < 0.001). the mean score in the different age groups fell significantly with increasing age (f = 5.965, p < 0.001) and there was a significant rise with the increase in educational level (f = 99.843, p < 0.001) ( table 2) . of the participants, 11.9% met the qualified standard of behavior. males had a significantly higher qualified proportion table 3 the qualified proportions for knowledge, behavior, and skill about influenza among respondents group of behavior than females (chi-square = 13.066, p < 0.001) and there was a significant rise with increasing educational levels (chisquare = 61.584, p < 0.001) ( table 3 ). urban residents had a significantly higher mean score for skill than rural residents (f = 428.286, p < 0.001). the mean score for the different age groups fell significantly with increasing age (f = 217.352, p < 0.001) and increased significantly with higher educational levels (f = 770.232, p < 0.001). there was a significant difference among the three occupational status levels (f = 21.669, p < 0.001), with the group of students having the highest mean score (2.57 ae 1.27) and the non-working group having the lowest mean score (2.14 ae 1.30) ( table 2) . of the participants, 43.4% met the qualified standard of skill. the qualified proportion of skill in urban residents was significantly higher than in rural residents (chi-square = 125.588, p < 0.001). the qualified proportion in the different age groups fell significantly with increasing age (chi-square = 477.533, p < 0.001) and increased significantly with higher educational levels (chi-square = 1322.136, p < 0.001). there was a significant difference among the three occupational status levels (chisquare = 31.165, p < 0.001), with the group of students having the highest qualified proportion (53.9%) and the non-working group having the lowest qualified proportion (40.6%) ( table 3) . there were positive correlations between knowledge and behavior, and knowledge and skill, which were statistically significant (p < 0.001). however, the extent was weak, as the correlation coefficients were r = 0.084 and r = 0.102, respectively (table 4 ). in recent years, pandemic influenza, as a global public health problem, has caused worldwide concerns. 8, 9 many previous studies have shown that the risk of seasonal or pandemic influenza infection depends on biological characteristics, individual or collective behaviors, and the environmental context. 10 research has been done on the knowledge, attitudes, and practices (kap) related to pandemic influenza a (h1n1) 2009 among the chinese general population, 11 but a related study has not been reported from beijing. this study could provide some important information to fill the gaps in this field. it was necessary and valuable for us to conduct the study to determine the overall level of influenzarelated health literacy in the general population of beijing after the 2009 pandemic, data that provide a baseline for influenza prevention and control strategies in the future. furthermore, our assessment may help shape policy and provide information to the international community. in this study we found that the qualified proportion of urban residents was significantly higher than that of rural residents; this was considered to be associated with socio-economic factors, such as income and medical resources allocation, 12,13 as well as the ability to access health information. the socio-economic status in rural areas is significantly lower than in urban areas; rural residents are always less likely to obtain the recommended preventive healthcare services, 14 and their limited ability to acquire information via modern media systems 15 impedes the dissemination of health information among rural dwellers. in addition, most public education activities are currently carried out in the communities of urban districts, hence the public awareness of influenza-related knowledge, behavior, and skill of rural residents is lower than that of urban residents. in this study, education was found to be the most important factor influencing levels of infectious disease health literacy, and past research on the relationship between education and health has drawn similar conclusions. howard et al 16 found that if health literacy levels were similar, differences in self-reported health status by education would be about 20% lower. there is also some indirect evidence. goldman and smith 17 found that well-educated patients are better able to manage complicated self-care regimens in hiv/aids and diabetes. other studies have found that education is linked to faster adoption of new medical technologies 18 and that consumer knowledge is linked to the increased use of preventive care. 19 in this study, the qualified levels of all three sections (knowledge, behavior, and skill) in the general population were significantly higher (p < 0.001) with a higher level of education, which is similar to the nationwide health literacy level of china. 20, 21 at present, different intervention strategies aimed at populations with different levels of education should be implemented. compared with younger people, the older age groups had worse health literacy related to influenza. the qualified proportion in the older age group was significantly lower than that in the younger group. older adults have lower immunity and ability to fight off disease and are at higher risk of becoming infected with influenza viruses. the risk of influenza-related complications and deaths among the elderly are significantly higher than in younger people. 22 the results of beijing's sixth population census showed the proportion of elderly (!60 years) to be 12.5%, 23 demonstrating that beijing has already become an aging society. the statistics in this study indicated that the influenza-related health literacy level among elderly residents in beijing was low. as a high-risk and susceptible population, the elderly should be paid more attention with regard to influenza prevention and control. there were positive correlations among knowledge, behavior, and skill about influenza, but the extent was weak. this indicates that there is still a gap in knowledge, behavior, and skill. full knowledge about the prevention of influenza does not mean reasonable behavior or skill. it is necessary to carry out various types of health education program aimed at behavior and skill. the study has a few limitations. first, some data were selfreported, which could have led to problems of recall bias. second, this study was a sampling survey, which will inevitably have had a sampling bias. however, because the participants were selected from communities by strict random sampling, it is believed that they do represent the general population of beijing. thirdly, there were no baseline data for influenza-related health literacy in the general population of beijing for the pre-pandemic period, so we cannot know whether the health literacy level of people was improved after in recent years, pandemic influenza, as a global public health problem, has caused worldwide concerns. 8, 9 many previous studies have shown that the risk of seasonal or pandemic influenza infection depends on biological characteristics, individual or collective behaviors and the environmental context. 10 as there has been no related study reported in beijing, this study could provide some important information to fill gaps in this field. it was necessary and valuable for us to conduct the study to determine the overall level of influenza-related health literacy in the general population of beijing after the 2009 pandemic, data that provide a baseline for influenza prevention and control strategies in the future. furthermore, our assessment may help shape policy and provide information to the international community. in conclusion, following the h1n1 2009 pandemic, the general population of beijing has some correct knowledge, practices, and skills related to influenza, however this health literacy level is low and the extent of relativities in knowledge, behavior, and skill about influenza was found to be weak. improvements are needed in terms of certain aspects, particularly for the elderly and the population of rural districts. educational level, as a significant factor in reducing the spread of influenza, should be considered seriously when intervention strategies are implemented, and we should provide more individual health counseling and education services for residents. world health organization. global alert and response (gar): pandemic (h1n1) 2009-update 112. geneva: who pandemic potential of a strain of influenza a (h1n1): early findings the first pandemic of the 21st century: a review of the 2009 pandemic variant influenza a (h1n1) virus world health organization. h1n1 in post-pandemic period. geneva: who response to the first wave of pandemic (h1n1) 2009: experiences and lessons learnt from china china's engagement with global health diplomacy: was sars a watershed health literacy as a public health goal: a challenge for contemporary health education and communication strategies into the 21st century pandemic influenza preparedness in the asia-pacific region wide spread public misconception in the early phase of the h1n1 influenza epidemic integrative study of pandemic a/h1n1 influenza infections: design and methods of the copanflu-france cohort knowledge, attitudes and practices (kap) related to the pandemic (h1n1) 2009 among chinese general population: a telephone survey an exploratory spatial analysis of pneumonia and influenza hospitalizations in ontario by age and gender equity and health sector reforms: can low-income countries escape the medical poverty trap? are rural residents less likely to obtain recommended preventive healthcare services? the construction and development status analysis on rural informationization in beijing impact of health literacy on socioeconomic and racial differences in health in an elderly population can patient self-management help explain the ses health gradient? the effect of education on medical technology adoption: are the more educated more likely to use new drugs? the role of consumer knowledge of insurance benefits in the demand for preventive health care among the elderly ministry of health of the people's republic of china. 2009, the first time chinese residents health literacy survey. beijing: ministry of health china association for science and technology. a survey of public scientific literacy in china. beijing: china association for science and technology geneva: who the sixth national population census this study was supported by grants from the beijing nova program of beijing science and technology commission conflict of interest: the authors declare that no conflict of interest exist. key: cord-311453-l6quzef6 authors: klopfenstein, timothée; zayet, souheil; lohse, anne; selles, phillippe; zahra, hajer; kadiane-oussou, n’dri juliette; toko, lynda; royer, pierre-yves; balblanc, jean-charles; gendrin, vincent; conrozier, thierry title: impact of tocilizumab on mortality and/or invasive mechanical ventilation requirement in a cohort of 206 covid-19 patients date: 2020-08-13 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.024 sha: doc_id: 311453 cord_uid: l6quzef6 introduction: no therapy has proven to be effective yet to reduce mortality and/or invasive mechanical ventilation (imv) requirement in covid-19. tocilizumab (tcz) in patients with severe covid-19 could be an effective treatment. method: we conducted a retrospective case-control study in the nord franche-comté hospital, france. we compared the outcome of patients treated with tcz and patients without tcz considering a combined primary endpoint: mortality and/or imv requirement. results: thirty patients were treated with tcz and 176 patients were treated without tcz. tcz was used in patients in a critical condition (oxygen therapy flow at tcz onset was 10.5 l/min and 14/30 patients had ≥ 50% lung involvement on ct scan) as a rescue treatment (8/30 patients who died were not admitted in usc in regards to their comorbidities). however, mortality and/or imv requirement were lower in patients with tcz than in patients without tcz (27% vs 52%, p = 0.009). conclusion: despite the small sample size in the group tcz, this result suggests that tcz reduces mortality and/or imv requirement in patients with severe sars-cov-2 pneumonia. this notion needs to be confirmed and spread in the medical community. the spread of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) has now been threatening human health for months. intensive care unit (icu) capacities are challenged to face this outbreak (1) . data is particularly needed on treatments able to reduce mortality and the number of critical ill patients (2) . death mainly results from acute respiratory distress syndrome (ards) (3) . markers of inflammation such as c-reactive-protein (crp), ferritin, and interleukin-6 are significantly associated with mortality (4, 5) . coronavirus disease 2019 (covid-19)-related multiple-organ failure and ards are mainly caused by cytokine storm (6) . post-viral hyper-inflammation, which begins in the second week of the disease, seems to explain disease severity (7) . tocilizumab (tcz) is a recombinant humanized anti-interleukin-6 receptor (il-6r) monoclonal antibody used in the treatment of rheumatoid arthritis and systemic lupus erythematosus. several arguments show that tcz administered to patients with severe covid-19 could be an effective treatment to reduce mortality. by neutralizing a key inflammatory factor in the cytokine release syndrome (crs), this molecule may block the cytokine storm during the systemic hyperinflammation stage and reduce disease severity (8, 9) . studies comparing the outcomes of patients treated with and without tcz are scarce, and include small numbers of patients (10) . we have recently published a retrospective study including 45 patients treated in our hospital, which shows that tcz seems to reduce the number of covid-19 severe cases and/or mortality (11) . in this work, we aim to extend this study to our entire j o u r n a l p r e -p r o o f patient population with confirmed covid-19 to compare the outcome, especially in terms of need for invasive mechanical ventilation (imv) and/or mortality, between patients treated with tcz and without tcz. we have conducted a retrospective case-control study in nfc (nord franche-comté) hospital. on march 1 st , a first case of covid-19 was confirmed in our hospital. "standard treatment" was administered to patients requiring oxygen therapy: hydroxychloroquine or lopinavir-ritonavir therapy or corticosteroids and antibiotics. on april 1 st , in relation with the increasing medical literature data, the nfc hospital scientific medical committee including infectious diseases specialists, icu specialists, rheumatologists, biologists, and pharmacists, approved the off-label use of tcz in patients with general status deterioration despite well-conducted standard care. daily "tocilizumab multidisciplinary team meetings" were organized to discuss patients' eligibility to receive tcz. based on the medical literature, we checked several criteria before starting tcz treatment: no contraindication to tcz, confirmed covid-19 with real-time reverse transcription (rt)-pcr sars-cov-2 rna, failure of standard treatment, period since symptoms onset ≥ 5 days, oxygen therapy ≥ 4 liters/min, ≥ 25% of lung damages on chest computed tomography (ct) scan, and ≥ 2 parameters of inflammation or biological markers of mortality (with a high level) such as ferritin, crp, d-dimer, lymphopenia, and/or lactate dehydrogenase. the present work compares two groups of patients. the "tocilizumab group" (tcz group) included all patients (except patients already in intensive care unit with imv) whom received standard treatment and tcz (8mg/kg per dose, 1 or 2 doses). between april 1 st and may 11 th , 2020, we enrolled all adult patients who received tcz for confirmed covid-19 by rt-pcr sars-cov-2 rna. all patients receiving tcz were informed that this prescription was used outside of its marketing authorization indications; they were also informed that they could deny the administration of tcz. in practice, several patients received tcz when there were in critical condition j o u r n a l p r e -p r o o f as a rescue treatment; in order to judge the effectiveness of tcz administration we excluded patients who had received the first dose of tcz less than 24h before intubation and/or death. the standard treatment group (st group) included patients receiving standard treatment but without tcz. on average, patients received tcz seven days after admission in our hospital (11) , so we stopped the inclusion in the st group one week before tcz availability. we excluded patients who hadn't received the standard treatment. this group included all hospitalized adult patients with confirmed covid-19 rt-pcr sars-cov-2 rna between march 1 st and march 24 th , 2020. because patients from the tcz group were all critically ill patients, and for comparative purposes between the two groups, we excluded from the control group the patients with moderate disease (i.e. those hospitalized for less than 48 hours and/or patients without any covid-19 symptoms) and patients who were less than 50-year-old (as none of the patients in the tcz group was younger than 50 yearsold). in all patients, diagnosis of covid-19 was confirmed by rt-pcr on respiratory samples. briefly, viral rna was extracted using the nucleospin®rna virus kit (macherey-nagel) according to the manufacturer's instructions, and amplified by rt-pcr protocols developed by the charité (e gene) (12) and the institut pasteur (rdrp gene) (13) on lightcycler 480® (roche). we collected the following data from the medical files of patients in both groups: demographic characteristics, comorbidities and outcome. to increase statistical power, we chose a combined primary endpoint (mortality and/or imv requirement) to compare the two groups. continuous variables were expressed as mean and standard deviation (sd) and compared with anova test. categorical variables were expressed as number (%) and compared by χ 2 test or fisher's exact test between the two groups. a p-value < 0.05 was considered significant. we used the spss v24.0 software (ibm, armonk, ny, usa). we have included 30 patients in the tcz group. thirty-three patients with confirmed covid-19 were treated with tcz before intubation between march 1 st and may 11 th , 2020. three patients intubated less than 24 hours after tcz first administration were excluded. we included 176 patients out of 661 patients who were assessed for eligibility in the st group ( figure a) . concerning the tcz group, oxygen therapy flow at tcz onset was 10.5 l/min [1.5-15] , the time of first symptoms and of admission to tcz onset was respectively 11.7 days [5-21] and 6.5 days . patients had high serum levels of c reactive protein (crp) (mean 142 mg/l) and ferritin (mean 1496 ng/ml) at tcz onset. forty-seven percent of patients (14/30) had ≥ 50% lung involvement on ct scan. concerning tcz administration, 27 patients had 2 doses of tcz (second dose given 24 to 72 hours after the first dose) and only 3 patients received a single dose. no statistical differences were observed between the two groups (tcz and st) with regard to age, sex, and comorbidities (table 1) . our combined primary endpoint (mortality and/or imv requirement) was higher in the st group than in the tcz group (52% vs 27%, p= 0.009) ( figure b ). patients in the st group clearly required imv more often than patients in the tcz group (22% vs 0, p=0.004); however, no statistical difference was observed between the two groups in terms of mortality. the 8 patients who died in the tcz group were not admitted in usc in regards to their comorbidities. it's interesting to notice that none of the three patients intubated less than 24 hours after tcz first administration died (two were discharged and one was still hospitalized). furthermore, if we included these 3 patients, mortality and/or imv requirement was still higher in the st group than in the tcz group (92/176 [52%] vs 11/33 [33%], p= 0.046). despite the small sample size of the tcz group, the latter strongly suggests that tcz may reduce the number of mortality and/or imv in patients with severe sars-cov-2 pneumonia. our population is older, with more comorbidities, and a higher level of mortality than other studies with covid-19 patients (5, 14) . these results are probably explained by the exclusion of patients without hospitalization criteria and less than 50 years old (in order to have a comparable population with the tcz group). patients in tcz group seemed to be more severe than patients in st group. in tcz group, patients had a higher respiratory rate and a lower pao2/fio2 ratio at admission than st group but without statistical differences. biological findings at admission were worse in tcz group than st group especially for ferritin, d-dimer and lactate dehydrogenase which are known on high level as predictive of poor outcome. furthermore, during hospitalization patients with tcz required a higher level of oxygen therapy (l/min) than patients with st (11.8 vs 8.1, p <0.001). the two groups differ about standard treatment. lopinavir/ritonavir was only administered in "standard treatment" group. on the contrary, hydroxychloroquine and corticosteroids were more often administered in tcz group. this is explained by the local management during the crisis, in our hospital lopinavir/ritonavir was recommended in the beginning of the outbreak and after a few weeks was replaced by hydroxychloroquine. then, in the end of the first period of inclusion, corticosteroids were an alternative treatment. tcz was administered on average 12 days after covid-19 symptoms onset, after standard treatment failure. it was prescribed on average 6.5 days after admission, after standard treatment failure in most cases, in patients presenting comorbidities in 83% of cases and who were critically ill (mean oxygen flow of 10.5 l/min). however, compared with the st group, the occurrence of mortality and/or imv requirement was clearly lower (27% vs 52%, p= 0.009). none of our 30 tcz-treated patients needed imv. finding enough icu beds is highly challenging during the present covid-19 pandemic (1); tcz could be the key in the treatment of covid-19 cases to reduce icu admissions. it could also have a huge public health impact as well as an impact on reducing the human and economic cost of the outbreak. only few case reports and series have reported that repeated doses of tcz may improve the condition of critical patients (8, (15) (16) (17) (18) (19) (20) . only capra et al. reported a case-control study which shows that tcz decreases mortality rate in patients with covid-19 related pneumonia (10) . in their study, two out of 62 patients of the tcz group and 11 out of 23 in the control group died, patients receiving tcz showed significantly greater survival rate as compared to control patients with a hazard ratio for death at 0.035 (95% confidence interval, 0.004 to 0.347; p = 0.004), adjusting for baseline clinical characteristics. in a recent observational, controlled study of 154 patients with severe covid-19 illness requiring mechanical ventilation, tocilizumab was associated with a 45% reduction in the hazard of death (19). the same kind of results were found by rossotti et al. in a comparative analysis between seventy-four patients treated with tcz and 148 patients controls (20). the low number of patients included in our work in the tcz group may explain that the difference in mortality is not significant because of a lack of statistical power. however, the main reason is probably that we administered tcz in many cases as a rescue treatment in critical patients who were too old and comorbid to be transferred in icu. therefore, the 8 patients who received tcz and died were not admitted in icu due to their comorbidities. furthermore, we have already published that our patients who received tcz were older, presented more comorbidities and were more critically ill than a control group selected with the same methodology but in a shorter period of time (11) . the post-viral hyperinflammation onset on the second week of the disease seems to explain covid-19 disease severity. by neutralizing a key inflammatory factor in the cytokine release syndrome tcz may block the cytokine storm during the systemic hyperinflammation stage and reduce disease severity. we don't have data about the right timing for tcz administration, in our study tcz was administered on average 12 days after onset of symptoms. however, tcz should probably be administrated earlier in the second week of the disease. our study is retrospective with a low number of patients in tcz group. larger prospective randomized trials are required to confirm these findings. our results suggest that tocilizumab reduces mortality and/or invasive mechanical ventilation requirement in patients with severe sars-cov-2 pneumonia. this notion needs to be confirmed and spread in the medical community. all authors contributed to data analysis, drafting or revising the article, gave final approval of the version to be published, and agree to be accountable for all aspects of the work. conflict of interest. the authors declare that they have no conflict of interests. j o u r n a l p r e -p r o o f intensive care management of coronavirus disease 2019 (covid-19): challenges and recommendations clinical course and mortality risk of severe covid-19 pathological findings of covid-19 associated with acute respiratory distress syndrome hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (covid-19): a meta-analysis correction to: clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan, china the pathogenesis and treatment of the `cytokine storm' in covid-19 covid-19 illness in native and immunosuppressed states: a clinical-therapeutic staging proposal why tocilizumab could be an effective treatment for severe covid-19? the cytokine release syndrome (crs) of severe covid-19 and interleukin-6 receptor (il-6r) antagonist tocilizumab may be the key to reduce the mortality impact of low dose tocilizumab on mortality rate in patients with covid-19 related pneumonia tocilizumab therapy reduced intensive care unit admissions and/or mortality in covid-19 patients detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr first cases of coronavirus disease 2019 (covid-19) in france: surveillance, investigations and control measures clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study. the lancet tocilizumab treatment in covid-19: a single center experience tocilizumab, an anti-il6 receptor antibody, to treat covid-19-related respiratory failure: a case report first case of covid-19 in a patient with multiple myeloma successfully treated with tocilizumab covid-19 in a patient with systemic sclerosis treated with tocilizumab for ssc-ild the authors thank especially emmanuel siess, azzedine rahmani, charlotte bourgoin, elodie bouvier, julien lorenne and frederic deuze for their strong implication in the present work.they also thank the management team of the hospital nord franche-comté for having made available tocilizumab outside its approved indication and each member of the hnf hospital tocilizumab multidisciplinary team.special acknowledgements to all the physicians, caregivers (nurses and orderlies) and patients. key: cord-301085-tk2vvxj7 authors: askarian, mehrdad; mclaws, mary-louise; meylan, marysia title: knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of shiraz, iran date: 2006-07-11 journal: int j infect dis doi: 10.1016/j.ijid.2006.01.006 sha: doc_id: 301085 cord_uid: tk2vvxj7 objective: to measure levels of knowledge, attitudes, and practice toward standard precautions (sp) in medical practitioners of shiraz university of medical sciences affiliated hospitals in iran. method: in this cross-sectional study, knowledge, attitude, and practice related to sp among four medical staff groups – surgeons, surgical residents, physicians and medical residents – were assessed using a questionnaire. results: across the four medical staffing groups the median levels of knowledge ranged from 6 to 7 (maximum score 9), median attitude scores were high ranging from 35 to 36 (maximum score 45), while median practice scores were low, ranging from 2 to 3 (maximum score 9). a moderate relationship between knowledge and attitudes was found in surgical residents and medical residents (r = 0.397, p = 0.030 and r = 0.554, p = 0.006, respectively). no significant correlation was found between knowledge and practice between the groups. a significant but poor (r = 0.399, p = 0.029) relationship between attitude and practice was found in surgical residents. conclusion: specific training programs may have to target newly graduated medical practitioners to establish acceptance of appropriate practices that will enable them to adopt and adhere to sp while their older counterparts may require more intense continuous assistance. objective: to measure levels of knowledge, attitudes, and practice toward standard precautions (sp) in medical practitioners of shiraz university of medical sciences affiliated hospitals in iran. method: in this cross-sectional study, knowledge, attitude, and practice related to sp among four medical staff groups -surgeons, surgical residents, physicians and medical residents -were assessed using a questionnaire. results: across the four medical staffing groups the median levels of knowledge ranged from 6 to 7 (maximum score 9), median attitude scores were high ranging from 35 to 36 (maximum score 45), while median practice scores were low, ranging from 2 to 3 (maximum score 9). a moderate relationship between knowledge and attitudes was found in surgical residents and medical residents (r = 0.397, p = 0.030 and r = 0.554, p = 0.006, respectively). no significant correlation was found between knowledge and practice between the groups. a significant but poor (r = 0.399, p = 0.029) relationship between attitude and practice was found in surgical residents. conclusion: specific training programs may have to target newly graduated medical practitioners to establish acceptance of appropriate practices that will enable them to adopt and adhere to sp while their older counterparts may require more intense continuous assistance. # 2006 international society for infectious diseases. published by elsevier ltd. all rights reserved. a heightened understanding of transmission of blood-borne diseases in the mid-1980s [1] [2] [3] [4] [5] [6] to healthcare workers (hcws), including surgeons, physicians, and residents in training, and the importance of adherence to standard precautions (sp) is well accepted. adherence to sp is even more important with the emergence of infectious diseases, such as avian influenza, severe acute respiratory syndrome, and the threat of bioterrorism. 7 the problems of containing drugresistant organisms such as methicillin-resistant staphylococcus 8-10 and vancomycin-resistant enterococci from colonizing patients give a continuous reminder to hcws that adherence to sp is also pivotal to patient safety in terms of healthcare-associated infections. in 1996, the centers for disease control proposed guidelines for isolation precautions in hospitals, as new, two-tiered best practice of infection control precautions that are standard for all patients who are to be regarded as potential carriers of pathogenic microorganisms. 1,10 strict adherence to sp guidelines is necessary to prevent exposure to potentially life-threatening infections, 3,11-15 yet a high level of compliance with sp has been reported to be problematic worldwide. 3, 4, [16] [17] [18] [19] [20] medical practitioners, especially surgeons, are among high-risk healthcare workers for exposure to blood-borne or other infections during direct patient contact. [2] [3] [4] the purpose of our study was to measure the level of knowledge, attitude, and practice in surgeons and physicians in shiraz university of medical sciences affiliated hospitals. a cross-sectional survey was conducted in shiraz university of medical sciences, shiraz, iran between may and november 2003 of four groups of medical staff; the questionnaire was to be answered by physicians, surgeons, surgical residents, and medical residents. the questionnaire was prepared by an infection control expert, a pediatrician certified in infectious diseases, and a psychiatrist, and reviewed by experts from the iranian national expert group of infection control specialists. it consisted of questions on knowledge, attitude, and practice of the guidelines with respect to standard isolation precautions as described by the cdc. the questionnaire was pre-tested on a random sample of participants to ensure practicability, validity, and interpretation of responses. the validity of the questionnaire was assessed using the kuder-richardson test for reliability and cronbach's alpha internal consistency coefficient. items in the questionnaire included demographic data, specialty and status of medical practitioner (surgeon, physician, surgical, or medical resident), previous sp education, willingness to be trained, and nine questions pertaining to hand-washing, personal protective equipment, m. askarian et al. use of antiseptic solution, and disposal method for used syringes. responses to items for knowledge were ''yes'', ''no'', or ''don't know''. the questions used to assess attitude were in the format of the likert scale with responses that included ''very strong'', ''strong'', ''considerable'', ''weak'', or ''null'' and the five-point likert scale response for practice questions (always, often, sometimes, seldom, never). all responses in accordance with cdc guidelines 1,10 were given a score value of 1 for correct answers to the knowledge questions and when answers for practice questions were ''always'', while a score zero was assigned to all other answers. the total scores ranged from zero to 9. for attitude questions, a score of 5 was equivalent to the answer ''very strong'' and a score of 1 to ''nil'', therefore, the total score ranged from 9 to 45 ( table 1 ). the questionnaire was pre-tested on 21 randomly-selected members from the target population with high test-retest reliability (alpha = 0.73). descriptive and inferential statistics including significance tests, wilcoxon rank-sum test, kruskall-wallis test, and spearman correlation coefficient were performed using spss version 10.0. alpha was set at the 5% level. of the 250 questionnaires distributed, 155 (62%) were returned completed. participants included 78 senior medical staff (42 surgeons and 36 physicians) and 77 residents (41 surgical residents and 36 medical residents) ( table 2 ). there were more male, 73.8% ( p = 0.002) than female surgeons, while there was no significant ( p = 0.061) gender difference within the physicians, 54.8% males. neither were there significant differences in the proportion of male surgical residents (56.1%, p = 0.435) and male medical residents (58.3%, p = 0.317). the median age of all senior medical staff was 34 years (range 26-70 years) and 31 years (range 24-39 years) for all residents ( table 2) . regardless of the status of medical practitioners, the majority (85.9% senior practitioners and 87.0% residents) reported no previous formal sp education and most (87.2% senior practitioners and 88.3% residents) were willing to receive sp training ( table 2) . the median scores for sp knowledge for all medical practitioners ranged from 6 to 7, while the range of median scores for attitudes was from 35 to 36 and that for practices from 2 to 3 ( table 3 ). the median scores for knowledge and attitude were not significantly different ( p = 0.077 and p = 0.653, respectively) between surgeons (knowledge median 7.0 and attitudes median score 36) and physicians (knowledge median score 6.0 and attitudes median score 35); median scores for practices were less than half the possible total score of nine, although the median scores for surgeons, 3.0, and physicians, 3.0, were equal but differed significantly ( p = 0.036) ( table 3) . although median scores for knowledge and attitudes were moderate to high, surgeons were the only group where a knowledge, attitude, and practices related to standard precautions 215 moderate to strong (r = 0.748) relationship between knowledge and attitudes was significant ( p < 0.0001) while for other medical groups this relationship was poor ( table 4 ). the relationship between knowledge and practices for all practitioners was not significant, as was the case for attitudes and practices, where correlations were not significant for all practitioners except surgical residents, where the relationship was significant but not strong, r = 0.399 ( p = 0.029) ( table 4 ). all medical practitioners' levels of knowledge were high for the same six items that were answered correctly by at least three quarters of practitioners within each group (table 5) . few medical practitioners answered correctly that needles should not be bent before disposal with correct knowledge ranging from 27.8% (physicians) to 55.6% (medical residents). as few as 9.5% of surgeons and 9.8% of surgical residents correctly believed that betadine was not used as a hand washing antiseptic solution. less than three quarters of practitioners correctly knew that they had to wash hands before glove use with proportions of practitioners answering correctly ranging from 52.8% (physicians) to 70.7% (surgical residents). only two of nine attitudinal items were answered as ''very much'' by more than 75% of practitioners (table 6 ). these two items indicating good attitudes related to sp activities do not require effort or much persuasion; the proportion of practitioners washing hands after touching blood, body fluids, excretions and contaminated items ranged from 91.7% to 95.2%, and glove use for touching mucous membranes, proportions ranged from 69.4% to 95.2%. only one sp practice item, hand washing after touching contaminated items, was always practiced by 75.6% to 100% of practitioners (table 5) . a medical resident's knowledge towards sp was related to willingness to be trained ( p = 0.013) and a surgeon's practice of sp was related only to female gender ( p = 0.006). no other significant predictive relationships were found. m. askarian et al. adherence to standard precaution guidelines has been problematic for hcws universally. [2] [3] [4] this study was limited by its reliance on self-reporting rather than by observing compliance with sp by practitioners. however, self-reported attitudes towards sp and compliance were low. our poor compliance with many sp practices is not unique to our teaching hospitals, with similar results published in other centers. 3, 4, [17] [18] [19] [20] [21] while principles of sp should be strictly observed by surgeons and physicians for their own safety as well as setting leadership roles for their residents, success in the implementation of sp guidelines depends on many factors such as optimal awareness and a positive attitude in all hcws, and these goals are not reached without qualified personnel receiving continuing regular education, as has been repeatedly demonstrated in the literature. 4, [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] our study revealed that more than 80% of all medical practitioners had not received previous sp education, and that more than 80% were willing to be trained. these findings illustrate that sp practices are not behaviors readily adopted, even by those aware of the sp issue and moderate to low levels of attitudes. a revision of current medical curricula offered in iran may be required that mandates all medical students and hospital trainees attend infection control courses specific to their clinical terms. although all our medical practitioners reported a willingness to be trained, compliance behavior is complex. 33 some barriers to adherence observed internationally include inadequacy of equipment and facilities and difficulties of access to equipment, stressful working conditions, and the belief that practice of sp may interfere with patient care. 2, 23, [34] [35] [36] [37] [38] [39] [40] [41] influencing the iranian senior practitioner may require elements of other successful programs knowledge, attitude, and practices related to standard precautions 217 and innovative approaches, such as improved hospital infrastructure that offers an infection control awareness week with infection control auditors to inform about correct practices at the time incorrect practices are observed, freely available personal protective equipment, such as gowns, gloves and masks, with reinforcing posters but also staff seminars launched on a platform of the importance of consistent sp practice for personal protection in times of emerging diseases. systematic review of adherence to infection control guidelines in dentistry noncompliance with universal precautions and the associated risk of mucocutaneous blood exposure among danish physicians nurses' knowledge of and compliance with universal precautions in an acute care hospital knowledge and performance of the universal precautions by nursing and medical students in korea management of healthcare workers infected with hepatitis b virus, hepatitis c virus, human immunodeficiency virus, or other bloodborne pathogens. aids/tb committee of the society for healthcare epidemiology of america frequency of glove perforations and subsequent blood contact in association with selected obstetric surgical procedures knowledge, perceptions, and practice of nurses toward hiv+/ aids patients diagnosed with tuberculosis can antibioticresistant nosocomial infections be controlled? revised uk guidelines for the control of methicillin-resistant staphylococcus aureus in hospitals standard precaution--a new approach to reducing infection transmission in the hospital setting double gloving protecting surgeons from blood contamination in the operating room efficacy of double gloving as a protection against blood exposure in dermatologic surgery use of double gloves to protect the surgeon from blood contact during aesthetic procedures double gloving as self protection in abdominal surgery subjective effects of double gloves on surgical performance orthopedic trauma surgeons' attitudes and practices towards bloodborne pathogens effect of education on the use of universal precautions in a university hospital emergency department compliance with universal precautions in a university hospital emergency department survey on adoption of measures to prevent nosocomial infection by anesthesia personnel compliance with universal precautions among emergency department personnel: implications for prevention programs factors associated with compliance of critical care nurses with universal precautions: a pilot study compliance with universal precautions among physicians the infection control practices of general dental practitioners nurses' compliance with universal precautions before and after implementation of osha regulations universal precautions training of preclinical students: impact on knowledge, attitudes, and compliance multidrug-resistant bacteria infection control: study of compliance with isolation precautions in a paris university hospital universal precautions: improving the knowledge of trained nurses orthopedic surgery residents and the cdc and aaos hiv precautionary measures hiv-related knowledge and precautions among michigan nurses a training program in universal precautions for second-year medical students improved compliance with universal precaution in the operating room following an educational intervention compliance with recommended infection control procedures among canadian dentists: results of a national survey the prevalence of and factors related to, compliance with glove utilization among nurses in hospital univeriti sains malaysia testing the reliability and validity of a measure of safety climate compliance with universal precautions: knowledge and behavior of residents and students in a department of obstetrics and gynecology compliance with universal precautions by emergency room nurses at maharaj nakorn chiang mai hospital risk taking by healthcare workers variables influencing worker compliance with universal precautions in the emergency department the use and failure rates of protective equipment to prevent blood and bodily fluid contamination in the obstetric healthcare worker compliance with handwashing and barrier precautions this article is the result of a research project (81-1412) approved by the deputy of research of shiraz university of medical sciences and health services. we want to express our special appreciation to the respected research deputy who not only provided financial support, but also showed his interest in solving difficulties.conflict of interest: no competing interest is declared. key: cord-318181-xxc7vdnt authors: ahmed, anwar e.; al-jahdali, hamdan; alshukairi, abeer n.; alaqeel, mody; siddiq, salma s.; alsaab, hanan; sakr, ezzeldin a.; alyahya, hamed a.; alandonisi, munzir m.; subedar, alaa t.; aloudah, nouf m.; baharoon, salim; alsalamah, majid a.; al johani, sameera; alghamdi, mohammed g. title: early identification of pneumonia patients at increased risk of middle east respiratory syndrome coronavirus infection in saudi arabia date: 2018-03-14 journal: int j infect dis doi: 10.1016/j.ijid.2018.03.005 sha: doc_id: 318181 cord_uid: xxc7vdnt background: the rapid and accurate identification of individuals who are at high risk of middle east respiratory syndrome coronavirus (mers-cov) infection remains a major challenge for the medical and scientific communities. the aim of this study was to develop and validate a risk prediction model for the screening of suspected cases of mers-cov infection in patients who have developed pneumonia. methods: a two-center, retrospective case–control study was performed. a total of 360 patients with confirmed pneumonia who were evaluated for mers-cov infection by real-time reverse transcription polymerase chain reaction (rrt-pcr) between september 1, 2012 and june 1, 2016 at king abdulaziz medical city in riyadh and king fahad general hospital in jeddah, were included. according to the rrt-pcr results, 135 patients were positive for mers-cov and 225 were negative. demographic characteristics, clinical presentations, and radiological and laboratory findings were collected for each subject. results: a risk prediction model to identify pneumonia patients at increased risk of mers-cov was developed. the model included male sex, contact with a sick patient or camel, diabetes, severe illness, low white blood cell (wbc) count, low alanine aminotransferase (alt), and high aspartate aminotransferase (ast). the model performed well in predicting mers-cov infection (area under the receiver operating characteristics curves (auc) 0.8162), on internal validation (auc 0.8037), and on a goodness-of-fit test (p = 0.592). the risk prediction model, which produced an optimal probability cut-off of 0.33, had a sensitivity of 0.716 and specificity of 0.783. conclusions: this study provides a simple, practical, and valid algorithm to identify pneumonia patients at increased risk of mers-cov infection. this risk prediction model could be useful for the early identification of patients at the highest risk of mers-cov infection. further validation of the prediction model on a large prospective cohort of representative patients with pneumonia is necessary. middle east respiratory syndrome coronavirus (mers-cov) was first identified in saudi arabia in 2012. the diagnosis of this infection remains complex (al johani and hajeer, 2016; sung et al., 2016; ahmed, 2017a) and it has a high fatality rate (ahmed, 2017b, c; aleanizy et al., 2017; sherbini et al., 2017; kim et al., 2017) . the early detection and identification of individuals at high risk of a disease is the most effective strategy to improve patient clinical outcomes (ahmed, 2017a) and reduce the costs of testing, both physical and economic (ahmed et al., 2011 (ahmed et al., , 2013 . the real-time reverse transcription polymerase chain reaction (rrt-pcr) has been found to be valid and accurate for the evaluation of respiratory swabs, sputum, and other endotracheal aspirate material (corman et al., 2012a, b) . however, although rrt-pcr is the most accurate and sensitive test available at the authors' centers, absolute identification of mers-cov may require multiple clinical specimens from different sources and take days (corman et al., 2012a, b; anon, 2018a) . the saudi ministry of health (moh) has developed mers-cov visual triage guidelines to identify suspected cases (anon, 2018b) . the current guidelines include fever, respiratory symptoms, gastrointestinal symptoms, chronic diseases, and risk of exposure to mers-cov. in clinical practice, identifying high-risk individuals can be challenging, since most laboratory-confirmed mers-cov patients report common clinical risk indices to patients with other respiratory conditions. for instance, respiratory and gastrointestinal symptoms are common for both mers-cov and non-mers-cov patients (mohd et al., 2016) . thus, further exploration must take place to reduce the risk of mers-cov infection. a risk prediction model is urgently needed to stratify patients with suspected mers-cov. this may decrease the risk of virus transmission to others who are in close contact, for example healthcare workers, patients, and hospital visitors, by allowing the careful management of those who are potentially infected at an early stage of infection. developing a mers-cov prediction model may more efficiently aid physicians in identifying individuals at high risk and selecting the necessary test(s) to improve prevention and control measures. several methodological studies have shown that combining demographic characteristics with clinical, radiological, and laboratory information can improve risk assessment and diagnostic accuracy (ahmed et al., 2011 (ahmed et al., , 2013 sidransky, 2002; etzioni et al., 2003) . these previous studies used a linear combination to develop an algorithm that combines demographic characteristics, symptoms, and clinical, radiological, and laboratory findings to identify the highly suspected mers-cov cases. mers-cov was initially identified in a patient being treated for pneumonia in 2012 (zaki et al., 2012) , and since then, pneumonia and its symptoms have remained common characteristics in mers-cov patients (saad et al., 2014; choi et al., 2016) . the aim of this study was to develop and validate a reliable risk prediction model for the screening of suspected cases of mers-cov infection in patients who have developed pneumonia. a two-center, retrospective case-control study was conducted utilizing data from king abdulaziz medical city in riyadh (kamc-r) and king fahad general hospital in jeddah (kfgh-jed), saudi arabia. the data were obtained between september 1, 2012 and june 1, 2016. kfgh-jed experienced a mers outbreak between march and may 2014 (oboho et al., 2015) , and kamc-r experienced a large mers outbreak between june and august 2015 (al-dorzi et al., 2016) . both study centers applied the saudi moh case definitions (anon, 2018b) to identify suspected individuals in the population studied, and rrt-pcr was used as the gold standard test to diagnose mers-cov in multiple and different clinical specimens when necessary. mers-cov-related symptoms were common at both centers. the project received ethical approval from two independent ethics committees: the saudi moh (irb log number 16-230e) and king abdullah international medical research center (study number rc17/061), riyadh saudi arabia. during the study, the medical records of 829 subjects who were being assessed by rrt-pcr for suspected mers-cov were reviewed. the suspicion of mers-cov infection at both kamc-r and kfgh-jed was determined based on the saudi moh guidelines (anon, 2018b) . two groups were compared: patients who were positive and patients who were negative for mers-cov infection. in an effort to reduce heterogeneity between the study groups, only subjects with a lung infiltrate on chest x-ray and/or computed tomography (ct) scan of the chest were included in the analysis. thus, subjects who had no available results of a chest x-ray or ct scan of the chest were excluded. the initial screening for suspected mers-cov patients includes pneumonia (anon, 2018b) . most of the patients studied were evaluated for pneumonia immediately after presentation. the study excluded subjects who were less than 15 years of age (pediatrics/children), as defined in the saudi moh guidelines (anon, 2018b) , and excluded subjects who had upper respiratory tract infections (respiratory symptoms, positive or negative mers-cov rrt-pcr, and normal chest x-ray and ct scan of the chest). the final sample comprised a cohort of 360 subjects who had a lung infiltrate on chest x-ray and/or a ct scan of the chest, who were classified according to the results of mers-cov rrt-pcr. the case group consisted of 135 pneumonia patients who were positive for mers-cov infection, and the control group consisted of 225 pneumonia patients who were negative for mers-cov infection. cases were defined as patients with mers-cov pneumonia who had positive mers-cov rrt-pcr on nasopharyngeal aspirate and/ or bronchoalveolar lavage in addition to a lung infiltrate on chest xray and/or ct scan of the chest. controls were defined as patients with respiratory symptoms, a lung infiltrate on chest x-ray and/or ct scan of the chest, pneumonia, and negative mers-cov rrt-pcr result of nasopharyngeal aspirate and/or bronchoalveolar lavage. nineteen predictive variables were included: age, sex, fever (temperature !38 c), one composite respiratory symptom (the presence of cough, bloody cough, shortness of breath, or chest pain), one composite gastrointestinal symptoms (the presence of diarrhea, vomiting, or nausea), seven mers-cov potential risk factors (contact with sick patients or camels, severe illness (defined according to the patient's clinical status, 'yes/no', which is based on clinical judgment), diabetes, lung disease, liver disease, renal disease, and heart disease), and seven laboratory measurements (white blood cell (wbc) count (â10 9 /l), platelets (â10 9 /l), creatinine (mmol/l), bilirubin (mmol/l), alanine aminotransferase (alt; u/l), aspartate aminotransferase (ast; u/l), and albumin (g/ l)). the reference ranges for the laboratory measures were as follows: wbc count, 4-11 â10 9 /l; platelets, 150-400 â 10 9 /l; creatinine, 50-98 mmol/l; bilirubin, 3.4-20.5 mmol/l; alt, 5-55 u/l; ast, 5-34 u/l; albumin, 35-55 g/l. no serological tests were available at the centers for these patients. stata statistical software release 15, 2017 (statacorp. llc, college station, tx, usa) was used for the data analysis. the sample characteristics were recorded as the frequency and percentage, or as the mean ae standard deviation (sd). laboratory measurements were summarized as the median and 25th-75th percentiles. a subgroup analysis (chi-square test, independent samples t-test, or mann-whitney u-test) was used to identify unadjusted associations between demographic, clinical, and laboratory measurements according to mers-cov status. the performance of each bivariate predictor was further assessed by unbiased estimate, the area under the curve (auc), and its 95% confidence interval (ci). stepwise binary logistic regression was employed to develop a mers-cov risk prediction model and identify factors that could be used to estimate the probabilities of mers-cov infection. the goodness-of-fit of the final model was tested by hosmer-lemeshow procedure: a large p-value indicates that a model has a good fit. the discrimination ability between high and minimal risk of mers-cov infection of the final model was assessed by the auc and its 95% ci. a receiver operating characteristics (roc) curve was generated for the risk prediction model. two hundred random samples were drawn with replacements from the original study sample (n = 360). the model internal validity was assessed in these 200 samples by the auc and its 95% ci. optimal cut-off values of the probabilities for each model were determined using a generalized youden index (youden, 1950) . at these thresholds, it was possible to achieve the best balance between specificity and sensitivity. a total of 360 pneumonia patients were included in the analysis: 37.5% were confirmed mers-cov-positive and 62.5% were confirmed mers-cov-negative. the mean age at presentation was 55.9 years, with a standard deviation of 20.2 years; age ranged between 16 and 109 years. of the total sample, 6.9% had been in contact with a sick patient or camel, 60% had fever, 84.2% had at least one respiratory symptom, and 18.6% had at least one gastrointestinal symptom. the two groups were similar in the distribution of age (p = 0.220) and sex (p = 0.079). the characteristics of the sample can be found in table 1 . subgroup analyses are presented in tables 1 and 2. the chisquare test or the independent samples t-test revealed that sex (p = 0.079) and age (p = 0.220) were similar in the two groups. the risk of mers-cov infection was similar in patients with and without fever (p = 0.267), respiratory symptoms (p = 0.080), or gastrointestinal symptoms (p = 0.382). severe illness (p = 0.001), contact with a sick patient or camel (p = 0.001), diabetes (p = 0.001), heart disease (p = 0.007), and renal disease (p = 0.025) were significantly associated with an increased risk of mers-cov infection. the independent samples mann-whitney u-test revealed that the wbc count (p = 0.001) and platelet count (p = 0.006) were significantly lower in patients who were positive for mers-cov than in those who were negative for mers-cov infection. in contrast, creatinine (p = 0.001), bilirubin (p = 0.001), ast (p = 0.001), and albumin (p = 0.004) were significantly higher in patients who were positive for mers-cov than in those who were negative for mers-cov infection. alt (p = 0.352) was insignificantly higher in patients who were positive for mers-cov than in those who were negative for mers-cov infection. according to the individual roc curve analysis (table 3) , severe illness, diabetes, wbc count, creatinine, bilirubin, albumin, and ast were the most important predictors of mers-cov infection. a risk prediction model was developed using stepwise binary logistic regression (p 0.05). the model retained seven independent variables that were associated with increased odds of mers-cov (table 4 ). male sex (adjusted odds ratio (aor) 1.883, p = 0.043), contact with a sick patient or camel (aor 21.915, p = 0.001), diabetes (aor 2.703, p = 0.002), severe illness (aor 6.312, p = 0.001), low wbc count (aor 0.897, p = 0.001), high ast (aor 1.007, p = 0.007), and low alt (aor 0.995, p = 0.024) were found to have a significant impact on the prediction of mers-cov. the hosmer-lemeshow test indicated that this model fitted the data well (p = 0.592). this model showed substantial discrimination, with an auc of 0.8162 and a 95% ci of 0.7651-0.8674 ( figure 1 ). the prediction model was validated using the bootstrap procedure. a total of 200 random samples were drawn with replacements from the original sample, and the model showed a substantial ability to assess mers-cov infection in this study population (auc 0.804, 95% ci 0.7838-0.8235). the findings in table 4 were used to create a risk-probability model. the risk prediction for the model can be expressed by the following equation: predicted probability = [1 + exp(1.409-(0.633 â male) à (3.087 â sick patient or camel contact) à (0.995 â diabetes) à (1.842 â severe illness) + (0.109 â wbc count) à (0.007 â ast) + (0.005 â alt))] à1 . a calculator was developed to calculate the potential risk of mers-cov infection in pneumonia patients. we determined the optimal cut-off or threshold values of the probabilities to mark the differences between the high-risk and low-risk groups. when an equal weight was given for sensitivity and specificity (m = 1), the optimal cut-off value (probability !0.33) produced sensitivity and specificity of 0.716 and 0.783, respectively. when more weight was given for sensitivity than specificity (m = 0.50), the optimal cut-off value (probability !0.20) produced sensitivity and specificity of 0.902 and 0.550, respectively. when more weight was given for specificity than sensitivity (m = 1.50), the optimal cut-off value (probability !0.39) produced sensitivity and specificity of 0.647 and 0.831, respectively. based on data from the two largest hospitals in saudi arabia, a risk prediction model was developed for mers-cov infection in pneumonia patients. this model was generated from a retrospective study and should be assessed prospectively for external validation. seven variables were identified as having a great impact on the mers-cov risk assessment prediction. the risk prediction model highlights the strong potential impact of male sex, contact with a sick patient or camel, severe illness, diabetes, low wbc count, high ast, and low alt on mers-cov infection. these few important parameters could be part of routine medical examinations to be performed (for the purpose of identifying highly suspected individuals) in daily clinical practice in order to make a prompt and timely clinical decision. according to the model, high ast was associated with an increased risk of being infected with mers-cov. this finding is similar to that of mohd et al., who noted high ast levels in mers-cov patients (mohd et al., 2016) . unlike their findings, it was noted in the present study that the impact of alt became significantly negative after controlling for several confounders. however, this type of association should be evaluated further in a prospective study in the presence of other unmeasured confounders. although sex was found to have no impact on mers-cov infection in the unadjusted analysis, the multivariate analysis revealed that the risk of mers-cov infection was 88.3% times higher in males than in females. this may be because other factors are playing a role in the development of mers-cov in males, such as camel contact, since males are more likely than females to have contact with camels. in agreement with the recent saudi moh mers-cov visual triage guidelines for the identification of suspected cases (anon, 2018b) , it was found that the odds of being infected with mers-cov were higher in patients with diabetes as compared to those with no diabetes. this also supports the findings of previous studies (badawi and ryoo, 2016; assiri et al., 2013; al-tawfiq et al., 2014; alraddadi et al., 2016) in which researchers systematically recognized that diabetes is a risk factor for mers-cov infection. these findings indicate that more attention should be given to assessing the risk of mers-cov infection in diabetic patients and whether the risk depends on a specific diabetes type or condition in these patients. as asserted in the saudi moh mers-cov visual triage guidelines and many other studies (muhairi et al., 2016; younan et al., 2016; reeves et al., 2015; sabir et al., 2016; azhar et al., 2014a, b) , contact with a sick patient or camel was identified as an independent predictor of mers-cov infection, according to the risk prediction model. it must be noted that the finding in the present study could have been limited by combining camel contact and sick patient contact due to the small sample size of each category. this study shows the importance of incorporating various types of information to improve the performance of the risk prediction. according to the linear combination model, it was found that several of the parameters highlighted in the saudi moh mers-cov visual triage guidelines were not able to distinguish between 'highrisk' and 'low-risk' groups, nor did they help in predicting mers-cov infection. for instance, fever, respiratory symptoms, gastrointestinal symptoms, heart disease, and renal disease were noted to have an insignificant impact on mers-cov infection. however, in agreement with the saudi moh mers-cov guidelines and two other reports (mohd et al., 2016; arabi et al., 2017) , the odds of being infected with mers-cov were associated with a significant risk reduction of 10.3% for each unit increase in wbc count. these results suggest that demographic, clinical, radiological, and laboratory data should be used in routine practice to identify suspected mers-cov cases, as such data could serve as the first line of prevention strategies. it was found that the accuracy of prediction (figure 1 ) was further improved when combining various medical and patient variables as opposed to relying on a single factor (table 3 ). this has been proven theoretically and in application (ahmed et al., 2013 (ahmed et al., , 2011 (ahmed et al., , 2015 etzioni et al., 2003; shen, 2008; pepe and thompson, 2000; su and liu, 1993; thompson, 2003) , where a linear combination has been used to maximize the diagnostic accuracy of a disease of interest. the strength of this study lies in the fact that a simple and applicable predictive model was developed that incorporates demographic, clinical, radiological, and laboratory data, where these were functionally associated and contributed greatly to stratifying and distinguishing between a high and a minimal risk of mers-cov infection. this simple evaluation of suspected mers-cov cases appears promising and could be implemented easily in routine clinical practice. this model could be used as a risk stratification method or a triage tool to help physicians in making an informed decision and planning the next step when deciding whether an rrt-pcr or further investigation is necessary. it was possible to derive a risk probability algorithm (range 0-1), a generalized youden index (choi et al., 2016) was used to determine an optimal cut-off to stratify the risk, and a risk probability of !0.41 was identified as being the optimal cut-off, with a sensitivity of 0.688 and specificity of 0.789. several limitations to the proposed risk prediction model were identified. the study findings were based on a retrospective design; therefore this prediction model should be interpreted with caution. limited information was available on patient variables, clinical variables, and transmission routes. for example, information on primary cases and secondary cases may be supplemented by the results of clinical, radiological, and laboratory data. in this study, 'contact with a sick patient' and 'contact with a sick camel' were combined into one variable due to the small number in each category. severe illness was based on a subjective judgment. an additional potential limitation was that the duration of symptoms was not available for these patients. this study investigated a very specific population (pneumonia) at only two centers, which could compromise the applicability and generalizability of the risk prediction model. moreover, the prediction model may not be generalizable to patients who do not fulfill the moh guidelines. further validation of the prediction model on an external sample and prospective cohort of representative patients with pneumonia is necessary, specifically in relevant settings: emergency, outpatient, inpatient, and community. despite these limitations, the model developed shows promise for the identification of suspected mers-cov cases in clinical practice. this model could be applicable in various healthcare settingsinpatient, outpatient, and emergency departmentsbecause no extensive laboratory testing is required and samples may be available within short turnaround times. this may allow rapid evaluation and improve clinical decision-making. in conclusion, this study provides a simple, practical, and valid algorithm to identify individuals at increased risk of mers-cov infection among patients who have developed pneumonia. this risk model is not only useful for risk stratification and decisionmaking in clinical practice, but it could also be useful in preventing and managing the possible spread of mers-cov. the usefulness of this 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index for rating diagnostic tests mers and the dromedary camel trade between africa and the middle east isolation of a novel coronavirus from a man with pneumonia in saudi arabia the authors acknowledge the saudi ministry of health and king abdullah international medical research center for approving this research project. the authors would like to thank the leaders of king abdulaziz medical city in riyadh and king fahad general hospital in jeddah for their support and understanding. supplementary data associated with this article can be found, in the online version, at https://doi.org/10.1016/j.ijid.2018.03.005. key: cord-277640-vy7ex5lv authors: calderaro, adriana; arcangeletti, maria cristina; de conto, flora; buttrini, mirko; montagna, paolo; montecchini, sara; ferraglia, francesca; pinardi, federica; chezzi, carlo title: sars-cov-2 infection diagnosed only by cell culture isolation before the local outbreak in an italian seven-week-old suckling baby date: 2020-05-14 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.035 sha: doc_id: 277640 cord_uid: vy7ex5lv sars-cov-2 is emerged in china on december 2019 and now declared pandemic by who. we describe the case of an italian 7-week-old suckling baby sars-cov-2-positive only by cell culture method with no clinical suspicion and/or risk factors of sars-cov-2 infection. the patient was referred to the hospital with signs and symptoms of infection of the upper respiratory tract before the virus was spread to the province. nasal and pharyngeal swabs and a nasopharyngeal aspirate were used for conventional and molecular diagnostic assays not including sars-cov-2 virus. bacteria referred to resident population were revealed in nasal and pharyngeal swabs. no viruses were detected using both immunofluorescence assay and nucleic acid amplification assays in the nasopharyngeal aspirate. the baby was discharged in good conditions after 3 days of hospitalization. later a cytopathic effect on the cell monolayers currently used for respiratory viruses was observed and the viral particles were identified as coronaviridae by transmission electron microscopy. sars-cov-2 was identified by rt-pcr performed both on cell culture and on the stored aliquot of the original sample. the virus isolate was named sars-cov-2/human/parma/1/2020.cell culture still remains the only reference diagnostic method also for emerging viruses, allowing to reveal cytopathogenic viruses and demonstrating their infectivity. a novel coronavirus was initially detected in wuhan (china) starting from december 2019 in patients with severe pneumonia of unknown origin (chen and yu, 2020) . genome sequencing allowed to classify the virus into the subgenus sar-becovirus of the genus betacoronavirus; it was termed as severe acute respiratory syndrome coronavirus 2 (sars-cov-2) and the illness it causes as coronavirus disease 2019 (covid-19). on march 11, 2020 the world health organization declared sars-cov-2 pandemic, considering the over 118,000 cases of the coronavirus illness in over 110 countries around the world (world health organization, 2020). the first case of sars-cov-2 infection in northern italy was assessed on 7 february, 2020 in a chinese subject recently returned from wuhan, but the infection has become epidemic in northern italy since february 21, 2020, when autochthonous cases have been identified (spiteri et al., 2020) . at the date of manuscript submission, italy was the second country with the highest number of sars-cov-2-infected subjects after usa (ministero della salute, 2020). in the area of parma, where our laboratory is located, sars-cov-2 became epidemic on march 3, 2020, and has reached 2083 cases on april 3, 2020. older age and comorbidities were associated with more severe clinical pictures, while the clinical course was generally milder in young subjects. available data regarding the clinical symptoms of the infection were mostly obtained from the elderly or subjects aged > 18 years old (salehi et al., 2020 , huang et al., 2020 . to the best of our knowledge, no literature evidence of sars-cov-2 virus infection diagnosed including virus isolation is present for suckling babies and very little evidence for new-borns (lu and shi, 2020, wang et al., 2020); in these reported cases, laboratory diagnosis was only done by molecular methods. here we describe the case of a seven-weekold suckling baby infected by of sars-cov-2 virus presenting fever and polypnea. the patient was referred to the neonatology ward of the university hospital of parma (italy) in the night of only the culture isolation of this cytopathogenic agent allowed its final identification as sars-cov-2. indeed, the clinical characteristics of the case and the time period in which the little patient came to the medical observation did not allow to suspect this specific infection, making it unnecessary to submit the baby to chest radiographs and ct scan; the baby has been discharged from the hospital in good conditions on february 28, 2020, and remained healthy in the following weeks. pharingeal swabs at 2 consecutive days were performed by the public service of health, 2 weeks after his discharging from the hospital, and both resulted negative for sars-cov-2 rna. the origin of the infection of the baby remains not clear; in the period before the admission to the hospital the parents were healthy, although the mother declared a slight malaise didn't stop her from breastfeeding they have never been tested for sars-cov-2 because they resulted healthy until march 17, 2020. however, after the baby was discharged, they remained at home in self-isolation, together with the baby. to the best of our knowledge, in the international literature at the time of the manuscript submission, no other reports of infants of this age describing the laboratory diagnosis of sars-cov-2 infection including virus isolation together with rna detection were present. the presented results highlight the importance of viral culture, to be used in parallel to molecular techniques, being the only reference laboratory method able to reveal the presence of cytopathogenic viral agents and demonstrating their infectivity also in case of emerging viruses. this is of relevance in those cases, such as the one described here, in which the symptoms are mild and the laboratory becomes an essential support to promptly report the presence of this pandemic virus for preventing its spread. this result stimulates not to limit the diagnosis to molecular tools in all the this study was supported by the ministry of university and scientific research grant fil, parma. italy the samples analysed in this study were sent to the university hospital of parma for routine diagnostic purposes, and the laboratory diagnosis results were reported in the medical records of the patients as answer to a clinical suspicion; ethical approval at the university hospital of parma is required only in cases in which the clinical samples are to be used for applications other than diagnosis. matrix-assisted laser desorption/ionization time-of-flight identification of different respiratory viruses matrix assisted laser desorption/ionization time of flight mass spectrometry first two months of the 2019 coronavirus disease (covid-19) epidemic in china: realtime surveillance and evaluation with a second derivative model coronaviridae study group of the international committee on taxonomy of viruses. the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 epidemiology of human respiratory viruses in children with acute respiratory tract infection in a 3-year hospital-based survey in northern italy coronavirus disease (covid-19) and neonate: what neonatologist need to know novel coronavirus (covid-19) situation coronavirus disease 2019 (covid-19): a systematic review of imaging findings in 919 patients a case report of neonatal covid-19 infection in china world health organization. coronavirus disease (covid-19) outbreak the authors declare no competing interests. ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-300774-5mrkmctl authors: hernández-mora, miguel górgolas; cabello úbeda, alfonso; pérez, laura prieto; álvarez, felipe villar; álvarez, beatriz álvarez; rodríguez nieto, maría jesús; acosta, irene carrillo; ormaechea, itziar fernández; al-hayani, aws waleed mohammed; carballosa, pilar; martínez, silvia calpena; ezzine, farah; gonzález, marina castellanos; naya, alba; de las heras, marta lópez; rodríguez guzmán, marcel josé; guijarro, ana cordero; lavado, antonio broncano; valcayo, alicia macías; garcía, marta martín; martínez, javier bécares; roblas, ricardo fernández; piris pinilla, miguel ángel; alen, josé fortes; pernaute, olga sánchez; bueno, fredeswinda romero; frades, sarah heili; romero, germán peces barba title: compassionate use of tocilizumab in severe sars-cov2 pneumonia date: 2020-10-25 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.045 sha: doc_id: 300774 cord_uid: 5mrkmctl introduction: tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe sars-cov-2 pneumonia (ssp), aiming to ameliorate the cytokine release syndrome (crs) -induced acute respiratory distress syndrome (ards). however, there are no consistent data whom might benefit most from it. methods: we provided tocilizumab on a compassionate-use basis to patients with ssp hospitalized (excluding intensive care and intubated cases) who required oxygen support to have a saturation >93%. primary endpoint was intubation or death after 24 hours of its administration. patients received at least one dose of 400 mg intravenous tocilizumab during march 8-2020, through april 20-2020. results: a total of 207 patients were studied and 186 analysed. the mean age was 65 years and 68% were male. a co-existing condition was present in 68 % of cases. death prognostic factors were older age, higher il-6, d-dimer and high sensitivity c reactive protein (hscrp), lower total lymphocytes and severe disease requiring higher oxygen support. the primary endpoint (intubation or death) was significantly worst (37% vs 13%, p < 0·001) in those receiving the drug when the oxygen support was high (fio2 > 0.5%). conclusions: tocilizumab is well tolerated in patients with severe sars-cov-2 pneumonia, but it has a limited effect on the evolution of cases with high oxygen support needs. tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe sars-cov-2 pneumonia (ssp), aiming to ameliorate the cytokine release syndrome (crs) -induced acute respiratory distress syndrome (ards). however, there are no consistent data whom might benefit most from it. we provided tocilizumab on a compassionate-use basis to patients with ssp hospitalized (excluding intensive care and intubated cases) who required oxygen support to have a saturation >93%. primary endpoint was intubation or death after 24 hours of its administration. patients received at least one dose of 400 mg intravenous tocilizumab during march 8-2020, through april 20-2020. a total of 207 patients were studied and 186 analysed. the mean age was 65 years and 68% were male. a co-existing condition was present in 68 % of cases. death prognostic factors were older age, higher il-6, d-dimer and high sensitivity c reactive protein (hscrp), lower total lymphocytes and severe disease requiring higher oxygen support. the primary endpoint (intubation or death) was significantly worst (37% vs 13%, p<0·001) in those receiving the drug when the oxygen support was high (fio2 >0.5%). since december 2019 the sars-cov-2 pandemic has affected more than 12,5 million people worldwide and more than 560,000 fatalities have been recorded [1] at the time of writing. patients with severe sars-cov-2 pneumonia (ssp) die due to poor oxygenation despite ventilatory support and different treatments including drugs with anti-viral activity, such as remdesivir, lopinavir/ritonavir, interferon beta, hydroxychloroquine; and/or anti-inflammatory drugs, such as corticosteroids, azithromycin and low molecular weight heparin amongst other [2] [3] [4] [5] . pathological post-mortem samples of lung and bone marrow of these patients show diffuse alveolar damage with alveolar edema, hyaline membranes and microvascular thrombosis along with extensive hemophacytosis in the bone marrow [6] . laboratory data show high levels of ferritin, interleukin-6, c-reactive protein, ldh and d dimer, all indicative of a cytokine release syndrome (crs) -induced ards [7] [8] [9] [10] derived from the viral infection. it is believed that the severity of sars-cov-2 pneumonia depends not only on the viral load in lung tissue but mainly on the inflammatory response of the host. interleukin-6 is a key factor for the activation of the cis-and trans-signaling pathways leading to the cytokine release syndrome [11, 12] . tocilizumab (tcz) is an interleukin 6 receptor antagonist which has been used for the treatment of rheumatoid arthritis [13] and for the treatment of chimeric antigen receptor (car) t cell-induced crs in cancer patients [14] [15] [16] . information about its use for sars-cov-2 pneumonia is limited [17, 18, 30, 31] and results of randomized clinical trials are still pending [19, 20] . we present a cohort of 207 patients treated with tcz at a single institution during the covid-19 outbreak in madrid with the aim to identify which clinical or laboratory factors might influence the evolution of ssp in this group of patients and to evaluate the tolerance of this drug in this clinical entity. from 8 th of march until 19 th of april 2020 a total of 207 with severe sars-cov-2 pneumonia admitted to the fundación jiménez díaz university hospital in madrid received tcz. ssp was defined as the presence of unilateral or bilateral lung infiltrates with basal oxygen saturation below 94% in patients with confirmed positive covid-19 rt-pcr (viasure® sars-cov-2 real time pcr detection kit) in nasopharyngeal or throat swabs or, in the absence of microbiological confirmation, the existence of clinical (fever, cough, dyspnoea, fatigue, etc), radiological (lung infiltrates), epidemiological (close contact with documented patients) and laboratory data (lymphopenia, high levels of ferritin, high sensitivity c reactive protein (hscrp), ldh, interleukin-6, d-dimer) suggestive of covid-19 infection. tocilizumab was recommended as a rescue treatment for patients not improving after the initial three days of intensive therapy including pulse steroids and low dose cyclosporine (see above) and requiring a fio2 greater than 0.35% to achieve an oxygen saturation above 93%. a single dose of tcz [400 mg if weight <75 kg and 600 mg if >75 kg] was given intravenously. 17 patients with very severe disease (median fio2 1%, iqr:0·4-1) received one or two more consecutive doses if the drug was readily available. 29 patients received tcz with fio2 <0.35%, despite our protocol recommendation, due to their physician decision. ten patients received tcz when requiring high flow oxygen support (fio2 >1) and were not included in the analysis as they were being attended at the intensive care respiratory unit, just before intubation at the intensive care unit. none of the patients included in the study were at the intensive care unit at the time of tcz administration and none had any concomitant known acute or previous infection or contraindication for its use at the time of tcz administration (less than 50x10 9 platelets or less than 500 neutrophils per µl, alt or ast 5-fold elevations, or decreased renal function). data on patient´s oxygen-support at admission, before and after tocilizumab administration were recorded according to the standard clinical practice. laboratory values before tcz administration including absolute lymphocyte counts, serum ferritin, interleukin-6, high sensitive c reactive protein, d-dimer, serum creatinine, alt, ast, ldh and lipid profile were available for most cases. laboratory data after tcz administration were obtained in the range of 2 to 5 days after, and were not available in all cases. the primary endpoint was the need for intubation or death. eleven patients who required intubation or died within 24 hours after tcz administration were not included in the analysis (four died and 7 were intubated) because we believed that there was not enough time to evaluate the effect of the drug as most of them were in an extremely severe condition at the time of tcz administration, and these patients will be evaluated in another study of critical cases attended in intensive care. all patients signed an informed consent for the compassionate use of tcz before its administration. this study was approved by the medical ethics committee of the fundación jiménez díaz university hospital. all data were collected by the investigators who performed the statistical analysis. all patients who received at least one dose of tocilizumab between march 8, 2020 until april 20, 2020 were included in the study. distribution normality was assessed using the kolmogorov-smirnov test. normally distributed data were presented as mean (sd), nonnormally distributed data as median (iqr), and categorical variables as frequency (%). differences between groups were analysed by chi-square test for categorical data or one-way anova for continuous data. kaplan-meiers curves were used for survival studies. results are reported as point estimates and 95 percent confidence intervals. analysis were done with spss software version 24.0. in total, 207 hospitalized patients received at least one dose of 400 mg or 600 mg iv tcz between march 8, 2020 until april 20, 2020, of whom 21 were excluded of the analysis because required high oxygen flow before tcz administration (10 cases) or were intubated or died within the first 24 hours after tcz administration (11 cases) leaving 186 patients for the analysis. 169 (91%) patients received one dose, 16 patients two doses and 1 patient three doses. the main clinical characteristics of patients are summarized in table 1 . the mean age of patients was 65 years and 68% were male. 68% of patients had a co-existing condition, high blood pressure being the most prevalent (51%). at the time of tcz administration 114 (61%) patients required fio2 ≥0.5% and 72 (39%) required fio2 <0.5%. the main laboratory values before tcz administration showed a marked elevation of ferritin, interleukin-6 and c-reactive protein, d-dimer and a low absolute lymphocyte count. almost all patients (168p, 90·3%) had received antiretroviral drugs (lopinavir/ritonavir) for a median duration of 3 days (iqr:1-5). hydroxychloroquine or chloroquine sulphate had been administered to 97·8% of cases; cyclosporine to 89·2%, interferon beta-1b to 9·7% and lmwh to 96·2%. pulse methyl-prednisolone had been given to 95·7% of cases at a dose of 250 mg/day for one to three days before tcz. antimicrobial agents, either doxycycline or azithromycin was given to all patients for a minimum duration of 5 days. during a follow-up period of fifteen days 51 patients achieved the primary endpoint (intubation or death) 19 patients needed intubation (of whom 4 died) and 36 died (32 of whom were not intubated). the primary endpoint (intubation or death) was significantly different in the group receiving tcz when the oxygen support was high (fio2 >0.5 %) compare to those with fio2 ≤0.5% (37% vs 13%, p<0·001) (figure 1) ( table 2) . changes in laboratory data 2 to 5 days after tcz administration are shown in table 3 . a statistically significant decrease in the median serum ferritin and the median hscrp was observed. interleukin-6 and d-dimer median serum levels increased and the median absolute lymphocyte count remained stable. thirty-six patients died despite tcz treatment. the main demographic, clinical and laboratory data of patients who died and survived are shown in table 4 . patients who died were older (75·8 years versus 62·5, p<0·001), had any co-existing condition (89% vs 63%, p=0·003), specifically high blood pressure (69% vs 46%, p=0·12); had a higher mean interleukin-6 before and after treatment (389 vs 116, p=0.017, and 1168 vs 311, p<0·001 respectively), a higher mean hscrp after treatment (3·5 vs 2·0, p<0·009), a lower absolute lymphocyte count before and after treatment (633 vs 803, p=0.052, and 527 vs 860, p=0·001 respectively), and a higher median d-dimer before and after treatment (8,288 vs 2,045, p=0.027, and 7832 vs 3190, p=0·027 respectively). the global survival rate of those who received tcz was 81% (150p), and it was 94 % for those who received it when their oxygen support was with a fio2 ≤0.5%, and 72% when it was >0.5% (p=0,000). a total of 11 (5·9%) patients had serious adverse reactions related to tcz reported by their treating physicians, including increased hepatic enzymes (5 cases) or bilirubin (3 cases), increased creatinine (3 cases), hyperkalaemia (1 case), and headache (1 case). secondary acquired infections after tcz administration were documented in 13 cases (6·3%), including fungal (candida spp 7 cases, aspergillus spp 2 cases) and bacterial (pseudomonas aeruginosa 2 cases, klebsiella pneumoniae 2 cases, enterococcus spp 2 cases). sars-cov-2 has infected more than 12,5 million people and killed more than 560,000 and, as yet, there is a lack of effective therapy for this novel disease [21] . several antiviral drugs, such as remdesivir -an rna polymerase nucleotide analogue -and lopinavir/ritonavir -an hiv protease inhibitor -have been tested either in a limited number of cases or in small clinical trials showing some benefits (remdesivir) [3] or none at all (lopinavir/ritonavir) [2] . however, clinical and pathological studies of sars-cov-2 disease indicate that a systemic cytokine storm due to macrophage activation may be the leading cause of death in the vast majority of patients, usually occurring two to four weeks after primary infection [14] [22] [23] . therefore, immunomodulatory drugs have been used empirically with the aim of regulating and suppressing the inflammatory reaction that leads to multi-organ failure and death [11] [22] , and, in a recent trial, the j o u r n a l p r e -p r o o f use of dexamethasone has been effective for those requiring invasive mechanical ventilation [29] . at present, there are more than 50 trials under way with tocilizumab (clinicaltrials.gov) that will give clear information on the efficacy of this drug for severe covid-19 disease. in the meantime, cohort studies, as ours, and clinical reports, are the only source of available information. an initial report of 21 patients treated in china by xu et al showed clinical improvement in all cases without deaths or adverse effects [17] . however, compare to our series, their patients were a median of nine years younger and also had a lower proportion of concomitant diseases, factors that might explain our higher fatality rate. in addition, the mean il6 value of the patients in xu´s series is like that of our group of survivors, but significantly lower than that of those who died in our study. it is possible that the blockage of the il6r by tcz might require higher doses in patients with higher serum il6 levels. we could not evaluate this issue in our series as only a small proportion of our patients received two or more doses of tcz. a second cohort by luo et al of 15 patients, eight of them also treated with steroids as most of our patients, showed a higher mortality rate (3/15, 20%) particularly in those patients with higher c reactive protein levels before tcz administration [30] . our data show similar results, showing a worst prognosis for those with higher crp before and after tocilizumab treatment. however, other biomarkers such as il6 levels and total lymphocyte count, and the amount of oxygen support needed are also key factors for the prognosis of this infection. one of the larger cohort study published so far includes 179 subjects treated in different centres in italy [31] and they used the same composite endpoint as ours, that is the need for intubation or death. of note, both cohorts studied are similar in terms of age, comorbidities and severity of the disease, but not in the proportion of subjects treated with steroids, which is much higher in ours. despite this, the proportion of patients achieving the primary endpoint (intubation or death) is similar in both series, 25,7 % in guaraldi´s and 27,4 in ours. the proportion of new acute infections after tcz was lower in our series (6,3 %) compare to theirs (13%), even with the use of steroids and cyclosporine in our group of patients. this might be related to a different and prolonged use of antibiotics in our series, or perhaps to a lack of recorded information due to the retrospective nature of the study. of note, we did not observe any herpesvirus reactivation. in another large cohort study carried out in italy [34] , with 196 subjects included, they observed an improvement in the results in non-intubated patients, treated early, as in our cohort, with tocilizumab, methylprednisolone or both. several studies have shown improvements in median hospital stay or in respiratory and laboratory parameters [35, 36] . even in patients who required intensive care unit support and mechanical ventilation, other authors have reported significant benefits when tocilizumab was added to the treatment of patients [37] [38] [39] . despite these findings in several studies, the first study designed by the pharmaceutical company, the covacta trial, failed to meet its primary endpoint [40] . however, the company had recently announced [41] the efficacy of tocilizumab, with a reduction in the likelihood j o u r n a l p r e -p r o o f of needing mechanical ventilation in hospitalized patients with covid-19-associated pneumonia, in the empacta phase iii clinical trial [42] . a detailed analysis of these data would be required after its publication. the most significant result of our study, which should be evaluated in well-designed clinical trials, is that tcz administration in severe but not critical cases is associated with a good prognosis, avoiding disease progression in 94% of cases, and only 6% requiring intubation due to progressive respiratory insufficiency. in contrast, we have observed that when the drug is given in more critical cases, with higher oxygen support needs, its value is less clear, at least in this group of cases treated with a single dose of tcz and a multiple drug combinations including corticosteroids and cyclosporine. it is possible that higher or repeated tcz doses might have added additional benefits. mortality rates in hospitalised patients with ssp varies widely but it is around 15.1% -28% in spanish, italian and china studies [24, 32, 33] , significantly higher than that of our series of patient who received tcz early in the course of the disease, when fio2 requirement was below 0.5%. surrogate markers of macrophage activation, such as serum ferritin levels, interleukin-6 levels and high sensitivity c reactive protein changed after tcz therapy, indicating a reduction of the inflammatory process. as expected, the median interleukin-6 levels increased 48 hours after tocilizumab, as have been shown in previous reports [30, 31] . unfortunately, we do not have further data of these markers days or weeks after tcz treatment. as expected, elevated inflammatory markers are associated with poor prognosis, despite tcz use. most patients received only one dose of 400 mg tocilizumab, mainly because of shortage of the drug during the peak of the epidemic. seventeen patients received two or more doses of the drug showing similar outcomes than those who received a single dose. these data suggest that even 400 mg of tocilizumab might be adequate for reducing the acute inflammatory process in severe cases, however, critical cases might require higher or repeated doses, an issue that we could not evaluate in our cohort. the safety and tolerance of tocilizumab was good in previous studies of non sars-cov-2 patients [24, 25] . in our series, a small number of serious adverse events were reported and attributed by physicians to the drug. the acquisition of secondary nosocomial infections was detected in 13 patients (6·9%) being most of them lung or urinary tract infections of fungal or bacterial aetiology. however, all these cases had previously received systemic corticosteroids, cyclosporine and antibiotics, and most of them were admitted in the intensive care unit at the time the secondary infection was detected. these infections are probably due to the combination of these treatments and risk factors. this is notable because patients with rheumatoid arthritis or those receiving car-t cell therapy for cancer who are treated with long term use of tocilizumab are prone to infectious complications [25] [27, 28] but these seems not to be the case with single or limited tcz administration. our study has several limitations, basically due to the retrospective collection of data and the absence of a control group. firstly, the decision to administer tocilizumab was j o u r n a l p r e -p r o o f made by the medical team responsible for each patient, despite our treatment protocol. therefore, the clinical status of patients and the timing of drug administration after the onset of covid-19 symptoms were variable; initially it was indicated in very respiratory compromised patients and later it was prescribed much earlier, with lower fio2 support, letting us study its efficacy in this situation. secondly, the total amount of drug and number of doses that patients received were not uniform, due, as previously mentioned, to a shortage of the drug in the country during the peak of the epidemic. thirdly, most patients had received previous and/or concomitant drugs, including systemic corticosteroids and hydroxychloroquine which have anti-inflammatory properties. therefore, we could not properly assess the impact of these drugs on the overall response of patients treated with tocilizumab. finally, survival rates would also have been influenced by the uci committee decision whether a patient was eligible for intubation or not. only large randomized clinical trials will be able to determine the impact of different immunomodulatory or anti-inflammatory drugs administered simultaneously. in summary, our data support the use of tcz in severe sars-cov-2 pneumonia, in combination with corticosteroids and other immunomodulatory drugs such as cyclosporine. when the respiratory compromise is still not very severe the survival rate is high (94%) and there are very limited side effects and secondary infections. this research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. we would first like to express our deepest gratitude for the patients and their families, who in a time of grief have contributed to the understanding of this disease. we are also grateful to the whole team of physicians and health personnel for their tireless, altruistic dedication, strength and effort during the current pandemics. finally, we would like to acknowledge dr. frances williams, for her invaluable role as english editor, laura cereceda as data manager and drs sánchez-verde and rodríguez de lema for their contribution to graphical abstract. ethical approval this study was approved by the medical ethics committee of the fundación jiménez díaz university hospital. reference approval number: eo069-020. figure 1 . kaplan-meiers curves for primary endpoint (need of invasive ventilation or death) in patients treated with tocilizumab. the blue line represents the group of patients who 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entity leading to early death in sepsis impact of glucocorticoid treatment in sars-cov-2 infection mortality: a retrospective controlled cohort study efficacy and safety of subcutaneous tocilizumab versus intravenous tocilizumab in combination with traditional dmards in patients with ra at week 97 (summacta) fda approval summary: tocilizumab for treatment of chimeric antigen receptor t cell-induced severe or life-threatening cytokine release syndrome infections associated with immunotherapeutic and molecular targeted agents in hematology and oncology overall infection risk in rheumatoid arthritis during treatment with abatacept, rituximab and tocilizumab; an observational cohort study effect of dexamethasone in hospitalized patients with covid-19: preliminary report tocilizumab treatment in covid-19: a single cener experience tocilizumab in patients with severe covid-19: a retrospective cohort study baseline characteristics and outcome of 1591 patients infected with sars-cov-2 admitted to icus of the lombardy region clinical course and risk factors for mortality of ault inpatients with covid-19 in wuham, chiina: a retrospective cohort sutdy tocilizumab and steroid treatment in patients with covid-19 pneumonia experience with tocilizumab in severe covid-19 pneumonia after 80 days of follow-up: a retrospective cohort study pilot prospective open, single-arm multicentre study on off-label use of tocilizumab in patients with severe covid-19 tocilizumab among patients with covid-19 in the intensive care unit: a multicentre observational study tocilizumab for treatment of mechanically ventilated patients with covid-19 tocilizumab for treatment of patients with severe covid-19: a retrospective cohort study covacta trial raises questions about tocilizumab's benefit in covid-19 a study to evaluate the efficacy and safety of tocilizumab in hospitalized participants with covid-19 pneumonia j o u r n a l p r e -p r o o f table 3 . clinical, laboratory, imaging data and outcomes of patients with severe sars-cov-2 pneumonia treated with tocilizumab. before after p oxygen-support category -no.(%) 7 days after tocilizumab -fio2 -0.21% (ambient air) key: cord-344478-5gp7v1uh authors: rosenberg, eli s.; holtgrave, david r.; udo, tomoko title: clarifying the record on hydroxychloroquine for the treatment of patients hospitalized with covid-19 date: 2020-07-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.055 sha: doc_id: 344478 cord_uid: 5gp7v1uh nan to the editors, the study from arshad et al on the use of hydroxychloroquine, with and without azithromycin, for the treatment of inpatients with covid-19 in one healthcare system (henry ford health system) is a new entrant into the rapidly expanding literature on the treatment of this disease [1, 2] . the study's findings of a significant beneficial effect of hydroxychloroquine in the reduction of in-hospital mortality are not consistent with several recent studies and as authors of one of those studies we wish to share a few observations [2] [3] [4] . in the discussion section, arshad et al distinguish their study from our cohort study of 1,438 patients in 25 new york metropolitan region hospitals, which found a generally null association between these medications and mortality [1, 4] . in doing so, the authors make multiple statements that are not factually aligned with our published research. arshad et al state that the rosenberg et al "…study included patients who were initiated on hydroxychloroquine therapy at any time during their hospitalization. in contrast, in our patient population, 82% received hydroxychloroquine within the first 24 hours of admission, and 91% within 48 hours of admission." [1] . although we included those who received hydroxychloroquine or azithromycin at any time during hospitalization, we reported detailed information on length of time from admission to initiation of either therapy (as well as on dosage patterns). in fact, patients in our study had been generally initiated rapidly: "hydroxychloroquine was initiated at a median of 1 day (q1-q3, 1-2) following admission and azithromycin was given at a median of 0 days (q1-q3, 0-1)." [4] . this distribution is quite similar to that of the henry ford study. the authors next state the following about our work: "because treatment regimens likely varied substantially (including delayed initiation) across the 25 hospitals that contributed patients to the study, it is not surprising that the case-fatality rate among the new york patients was significantly higher than j o u r n a l p r e -p r o o f in our study." this statement neglects the extensive statistical adjustment for between-facility variation in our publication, the generalizability benefit of including 25 hospitals into the cohort with differing therapeutic protocols and approaches, and it misrepresents the fatality rate in our study. we reported 20.3% (95% ci: [18. .4%]) fatality from 292 deaths in 1,438 patients, whereas arshad et al report 18.1% from 460 deaths in 2,541 patients in a later era of the covid-19 epidemic. we fail to find a difference between these studies' fatality rates both practically and statistically ( 2 df=1 test p=0.09). these erroneous representations of previous work should be clarified as they have appeared to have led to confusion in subsequent characterizations of the arshad et al paper relative to our study [5, 6] . arshad et al study [7] . we underscore the concerns raised that bias may have been introduced into the inpatient treatment of covid-19 were stopped early due to lack of efficacy [9, 10] . on july 4, the who similarly halted the hydroxycholorquine arm of their solidarity trial [11] . evidence from recovery was a key factor weighed in the us food and drug administration's (fda) june 15 decision to revoke hydroxychloroquine's emergency use authorization (eua) for covid-19 treatment [12] . we appreciate the opportunity to clarify the record regarding our study as described by treatment with hydroxychloroquine, azithromycin, and combination in patients hospitalized with covid-19 swinging the pendulum: lessons learned from public discourse concerning hydroxychloroquine and covid-19. expert review of clinical immunology observational study of hydroxychloroquine in hospitalized patients with covid-19 association of treatment with hydroxychloroquine or azithromycin with in-hospital mortality in patients with covid-19 in treatment with hydroxychloroquine cut death rate significantly in covid-19 patients, henry ford health system study shows hydroxychloroquine saved lives among coronavirus patients 2020 an observational cohort study of hydroxychloroquine and azithromycin for covid-19: (can&#x2019;t get no) satisfaction effect of dexamethasone in hospitalized patients with covid-19: preliminary report no clinical benefit from use of hydroxychloroquine in hospitalised patients with covid-19 2020 nih halts clinical trial of hydroxychloroquine: study shows treatment does no harm, but provides no benefit 2020 who. who discontinues hydroxychloroquine and lopinavir/ritonavir treatment arms for covid-19 2020 letter revoking eua for chloroquine phosphate and hydroxychloroquine sulfate 2020 key: cord-317500-ufo2qgj4 authors: scialpi, michele; scialp, sara; piscioli, irene; scalera, giovanni; longo, fernando title: pulmonary thromboembolism in criticall ill covid-19 patients date: 2020-04-24 journal: int j infect dis doi: 10.1016/j.ijid.2020.04.056 sha: doc_id: 317500 cord_uid: ufo2qgj4 nan dear editor, the outbreak of novel coronavirus disease 2019 in the city of wuhan, hubei province of china, has been declared a pandemic by the world health organization (who) on march 21 st , and has since then forced the scientific community to consider two fundamental aspects: first off, sars-cov-2 does not only cause pneumonia and second, the death of many critical ill patients is caused by multiple organ failure (involving the heart, liver, kidneys, blood and immune system). therefore, attention should be paid to potential multiorgan injury and its prevention should be part of the treatment of covid-19 especially in critically ill patients (1). since the first report of dr zhu et al. in covid-19 infection, which is associated with a high morbidity and mortality rate, largerly due to respiratory failure, a pathophysiological role of pe and the usefulness of contrast-enhanced ct in diagnosis may be considered. comorbidities and multi-organ injuries in the treatment of covid-19 a novel coronavirus from patients with pneumonia in china ct imaging features of 2019 novel coronavirus (2019-ncov) time course of lung changes on chest ct during recovery from 2019 novel coronavirus (covid-19) pneumonia performance of radiologists in differentiating covid-19 from viral pneumonia on chest ct 2019-novel coronavirus severe adult respiratory distress syndrome in two cases in italy: an uncommon radiological presentation chest ct manifestations of new coronavirus disease 2019 (covid-19): a pictorial review acute pulmonary embolism and covid-19 pneumonia: a random association? covid-19 complicated by acute pulmonary embolism radiology: cardiothoracic imaging findings of acute pulmonary embolism in covid-19 patients prognostic factors for vte and bleeding in hospitalized medical patients: a systematic review and meta-analysis pii: blood american society of hematology 2019 guidelines for management of venous thromboembolism: prevention of venous thromboembolism in surgical hospitalized patients covid-19 and pulmonary embolism: frequentlyasked questions. americam society of haematology, covid-resources the use of anti-inflammatory drugs in the treatment of people with severe coronavirus disease 2019 (covid-19): the experience of clinical immunologists from china modified improve vte risk score and elevated d-dimer identify a high venous thromboembolism risk in acutely ill medical population for extended thromboprophylaxis. th open management strategy of novel coronavirus (covid-19) pneumonia in the radiology department: a chinese experience the authors declare no conflicts of interest associated for the manuscript entiltled "pulmonary thromboembolism in criticall ill covid-19 patients key: cord-317910-rwhwo55z authors: aziz, asma b.; raqib, rubhana; khan, wasif a.; rahman, mahbubur; haque, rashidul; alam, munir; zaman, k.; ross, allen g. title: integrated control of covid-19 in resource poor countries date: 2020-09-09 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.009 sha: doc_id: 317910 cord_uid: rwhwo55z low and middle income countries (lmics) face many challenges in controlling covid-19 in their countries. health-care resources are limited and so are icu beds. rt-pcr testing is conducted on a limited scale and treatment options are few. there is no vaccine. therefore, what low cost solutions remain for the prevention, diagnosis, and treatment of sars-cov-2? how should these essential health services be delivered in order to reach the most vulnerable in our societies? in this editorial we discuss several important strategies for controlling covid-19 including: vaccination, molecular and serological diagnostics, hygiene and wash interventions, and low-cost therapeutics. we also discuss the delivery of such services in order to reach the most in need. the proposed integrated control strategy requires immediate action and political will in order to reduce the widening health inequalities caused by the pandemic. there is intense global race to find a covid-19 vaccine. as of august 29 th 2020, 143 vaccine candidates are in preclinical evaluation and 46 candidate vaccines are being tested in human clinical trials (phase i-iii) [1, 2] . nine vaccine candidates have now entered phase iii trials in several countries utilizing thousands of volunteers. the phase iii candidates were developed by sinovac life sciences co., ltd, china (nct04456595), the university of oxford (isrctn89951424); cansino biologics, china (nct04526990), wuhan institute of biological products (chictr2000034780), beijing institute of biological products (chictr2000034780),modernatx inc., usa (nct04470427), gamaleya research institute, russia (nct04530396), biontech/fosun pharma/pfizer (nct04368728) and janssen pharmaceutical companies (nct04505722) [1] . to develop these vaccines, various new and old techniques have been used to produce immune response including genetic vaccines where one or more of the coronavirus's genes are used; viral vector vaccines where a virus (unable to replicate) is used to deliver coronavirus genes into cells to make viral proteins; protein-based vaccines using coronavirus spike protein or it's fragment; and whole-virus vaccines using weakened or inactivated viruses [2] . sinovac biotech, co. ltd beijing has developed a promising inactivated sars-cov-2 vaccine (vero cell) and tested it successfully in phase i/ii trial among 744 healthy chinese participants aged 18-59 years (nct04352608) (figure 1 ). the results from phase i/ii trials showed that a two-dose schedule of the vaccine was well-tolerated, safe (without any serious adverse reaction), and immunogenic (produced high titers of antibodies). sinovac is presently conducting phase iii trials in brazil, saudi arabia, turkey, chile, and indonesia and soon in bangladesh. according to many vaccinologists, inactivated vaccines may be the best choice against covid-19 as there is no risk of reversion to a virulent form. inactivated vaccines have been extremely effective over the past century to induce protection against many deadly viral pathogens such as polio, rabies, hav and influenza. another promising vaccine developed by the university of oxford is a chimpanzee adenoviral vectored coronavirus vaccine which was developed within 100 days after deciphering genetic sequence of the virus. the results published in the lancet showed that a single dose of vaccine was safe and immunogenic in phase i/ii trials [3] . oxford's commercial and manufacturing partner astrazeneca pharmaceutical already received advance orders for billions of doses worldwide. combined phase ii/iii trials and a separate phase iii study to test the safety and efficacy of the vaccine are being conducted among tens of thousands of participants in the uk, brazil, and south africa [4] . these two vaccine candidates have created hope that vaccine will be available for early 2021. there are still questions of whether these vaccines will be available for lmics or if vaccine production facilities will be adequate to assure a reliable supply within a suitable timeline frame to meet global demand. more specifically, there must be a transparent global allocation system to prioritize access to the vaccines at low cost for frontline healthcare workers and to people living in poorer countries with a higher risk of severe illness and death. as covid-19 is highly contagious (r0 2.5), we will need to vaccinate approximately 80% of the population with a vaccine with 80% proven efficacy. to ensure equity of access and international deployment we must support global randomized controlled trials of several leading vaccine candidates through the 'the who solidarity vaccines trials' [5] . to provide the vaccines free of cost to resource-poor nations we will need a global fund supported by the world bank, the gates foundation, the wellcome trust and g8 nations [6] . even if successful it is unlikely that vaccination will be a stand-alone strategy to control sars-cov-2 [7] . who has recommended nucleic acid amplification tests using rt-qpcr for the routine diagnosis of covid-19 infection [8] . this is the gold standard for diagnosing covid-19 and practiced all over the world including resource poor countries. however, most lmics are struggling to test samples and track the true infection rate due to a lack of laboratory facilities, trained manpower and regular supply of the rt-qpcr kits. so, the infection rate these countries are forecasting may actually represent only a tip of the iceberg. for example, at the beginning of covid-19 pandemic bangladesh had only one rt-qpcr laboratory at the institute of epidemiology and disease control research (iedcr) designated for diagnosis of covid-19 infection for the whole country (170 million) but now there are 77 rt-pcr labs ( figure 2 ) conducting approximately 20,000 daily tests [9] . lack of trained manpower capable of performing the molecular biology experiments (e.g. viral rna extraction and qpcr) required to testing covid-19 and interpreting the results are major limitations in resource poor countries. recently, several publications have reported the successful use of loop-mediated isothermal amplification (lamp)-based protocols to test for covid-19 in urine, saliva, as well as oropharyngeal and nasopharyngeal swabs both with or without the requirement of viral rna extraction [10] . so, alternative testing protocols, such as lamp, that utilize rapid antigen detection with limited resources and available manpower will be extremely useful. serological tests are comparatively easier to perform, and require less technical expertise and equipment compared to nucleic acid-based detection [11] . serological tests can complement rt-pcr in the diagnosis of acute infection, sick or hospitalized patients with severe symptoms who have tested negative with rt-pcr, or for determining the antibody status of healthcare professionals (and other workers) who are ready to return to work after being ill with covid-19. serological testing could also be used to investigate the attack rate of an ongoing outbreak in the community, detecting the prevalence of asymptomatic carriers and for the selection of donors of convalescent sera for treatment purpose [12] . at the national level, expanding testing capacity through antibody testing will enable large-scale screening at the population level generating crucial intelligence on estimates of disease spread and mortality attributable to covid-19 and ensure timely implementation of containment measures. due to the unprecedented demand for rapid diagnostic testing to enable the efficient treatment and mitigation of covid-19, the us fda has allowed expanding access to serology tests, by issuing emergency use authorization for serological tests [13] . one of the lab-based automated testing platforms for serological testing is elecsys® anti-sars-cov-2 by roche diagnostics which is a qualitative total antibody test (igm & igg), that detects antibodies against sars-cov-2 in patients using the necleocapsid protein. the elecsys assay has high clinical sensitivity (99.5%; ≥14 days' post pcr confirmation) and overall specificity (99.81%), resulting in highly reliable and accurate results. moreover, it is a quick test providing results within 18 minutes. combining such immunoassays with molecular diagnostics is deemed the best approach for bangladesh and other lmics and is presently being conducted in 21 states of india [14] . the directorate general of drug administration of bangladesh has not yet approved any serological tests for the country except for research purposes. in the absence of a vaccine to tackle covid-19 many repurposed drugs have been identified in observational series or are being used anecdotally based on in vitro or extrapolated evidence globally. to treat covid-19 patients, repositioning of old drugs for use as antiviral treatment is an intuitive strategy during the pandemic because the safety profile, side effects, posology, and drug interactions of these drugs are already established. this includes remdesivir, chloroquine, favipiravir, danoprevir, ritonavir, bromhexine hydrochloride, hydrochloroquine, convalescent plasma, and other interventions. in a resource-limited country such as bangladesh, we strongly feel that if such drugs are scientifically proven to be safe and effective they should be made available to the general population and free for indigent. the icddr, b is present conducting a randomized, doubleblind, placebo-controlled trial in three covid-19 dedicated hospitals in dhaka city comparing ivermectin and doxycycline in combination or ivermectin alone for the treatment of adult bangladeshi patients. the pharmaceutical industry in bangladesh continues to produce 98% of the medicines used domestically, and exports high quality drugs to over 150 countries, including europe and north america. this outstanding growth of the drug industry has occurred following the 1982 drug act of the government of bangladesh promoting the local pharmaceuticals. this resulted in local pharmaceuticals being able to produce inexpensive high quality generic drugs that don't require extensive and costly human trials. bangladesh, as an lmic, is exempt from patent restrictions till 2032 and is free to copy any drug on the market or in the pipeline, while more developed countries can only copy 'out of patent' drugs. because of this advantage, soon after abbott pharmaceutical announced one of its anti-viral drugs (remdesivir) showed good safety and efficacy against severe covid-19 in the usa, bangladeshi pharma were the first to make generic copies of the drug and export them globally. the rapid monitoring of covid-19 transmission pathways is required for prevention, intervention, and control. studies have shown that covid -19 viral rna can be persistently shed in the feces for a maximum of 33 days after the patient has tested negative for respiratory viral rna [15] . although it is yet to be confirmed that fecal-oral transmission is indeed possible [16] . therefore, safely managing fecal wastes from infected, recovering and recovered patients poses a significant challenge in developing countries and in urban slums. despite several uncertainties, new horizons are opening up as shown by recent reviews on testing for sars-cov-2 in wastewater for early detection and monitoring of outbreaks. thus far researchers have found traces of the sars-cov-2 in the sewage in the netherlands, australia, china, india, the united states and sweden. evidence on hand hygiene and influenza potentially provides a useful comparison for covid-19. a systematic review by saunders-hastings et al. (2017) shows frequent handwashing to have a large and significant protective effect against pandemic influenza [17] (figure 3 ). aiello et al. (2008) found that handwashing reduces the rate of respiratory infections by removing respiratory pathogens from the hands, and thus preventing them from entering the body or passing on to other people [18] . further evidence suggests that washing hands with soap after defecation and before eating can cut the respiratory infection rate by up to 25% [19] . ensuring convenient and accessible handwashing techniques are needed on entering or leaving the household and in public places especially after coughing or sneezing. a potential outbreak response program for covid-19 prevention could be deployed at three levels comprising: a mass strategy, a district/ward strategy and a household strategy. a 'mass strategy' could be deployed within a city or town where residents will be informed of the 'covid prevention program' in their respective district or ward via: sms text phone messages; local health centers; epi centers; pharmacies; and community notice boards. health education would focus on the risk factors for covid-19 and better cough hygiene practices. mass media, on covid-19 could showcase protect your family from covid-19 video to illustrate effective wash practices to lower risk. as part of a 'district/ward strategy' an early warning surveillance system may be deployed using: rapid diagnostic testing (e.g., roche antibody test for suspected covid cases) at health facilities and local hospitals; periodic testing of sewage systems for the presence of sars-cov-2 in municipality sewage water; android-based phone reporting of real-time test results; gis risk mapping of patients' addresses. a family emergency wash kit could be utilized as a 'household strategy' for families with a newly diagnosed family member. the kit for covid-19 could comprise: a prevention poster for the family on how to minimize the risk of acquiring and transmitting covid-19; 'soapy water' package (soap and 3 dispensers) enough for a family of five for 30 days; daily household disinfectant with bleach (3-6% sodium hypochlorite); and wearing of masks within the house. vaccination alone will not halt the covid-19 pandemic. low cost evidence-based integrated control strategies will be required. we must ensure access to reliable diagnostics in order to determine the true burden of disease in the community. to support the existing health system, data on the safety and effectiveness of locally available, affordable, and costeffective therapeutic drugs needs to be generated in order to treat covid-19 patient. a combination of effective vaccination, treatment and wash will ensure enhanced protection who's draft landscape of covid-19 candidate vaccines safety and immunogenicity of the chadox1 ncov-19 vaccine against sars-cov-2: a preliminary report of a phase 1/2, singleblind, randomised controlled trial covid-19: oxford team begins vaccine trials in brazil and south africa to determine efficacy world health organization solidarity vaccines trial expert group. covid-19 vaccine trials should seek worthwhile efficacy a win-win solution?: a critical analysis of tiered pricing to improve access to medicines in developing countries can we 'wash' infectious diseases out of slums? critical preparedness, readiness and response actions covid-102020-03-22_final-eng. pdf? sequence=1&isallowed=y directorate general of health services (dghs), government of bangladesh clinical evaluation of self-collected saliva by rt-qpcr, direct rt-qpcr, rt-lamp, and a rapid antigen test to diagnose covid-19 diagnostic performance of covid-19 serology assays presumed asymptomatic carrier transmission of covid-19 persistent viral shedding of sars-cov-2 in faeces -a rapid review covid-19: the environmental implications of shedding sars-cov-2 in human faeces effectiveness of personal protective measures in reducing pandemic influenza transmission: a systematic review and meta-analysis effect of hand hygiene on infectious disease risk in the community setting: a meta-analysis effect of washing hands with soap on diarrhoea risk in the community: a systematic review key: cord-308114-68cgub5o authors: afrin, lawrence b.; weinstock, leonard b.; molderings, gerhard j. title: covid-19 hyperinflammation and post-covid-19 illness may be rooted in mast cell activation syndrome date: 2020-09-10 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.016 sha: doc_id: 308114 cord_uid: 68cgub5o objectives one-fifth of covid-19 patients suffer a severely symptomatic, hyperinflammatory course, but specific causes remain unclear. mast cells (mcs) are activated by sars-cov-2. though only recently recognized, mc activation syndrome (mcas), usually due to acquired mc clonality, is a chronic multisystem disorder with inflammatory and allergic themes and estimated prevalence of 17%. we describe a novel conjecture explaining how mcas might cause propensity for severe acute covid-19 infection and chronic post-covid-19 illnesses. methods observations of covid-19 illness in patients with/without mcas, set against our extensive clinical experience with mcas. results the prevalence of mcas is concordant with the prevalence of severe cases within the covid-19-infected population. much of covid-19’s hyperinflammation is concordant with manners of inflammation which mc activation can drive. drugs with activity against mcs or their mediators have been preliminarily observed helpful in covid-19 patients. none of our treated mcas patients who have endured covid-19 infection have suffered severe courses of the infection, let alone mortality. conclusions hyperinflammatory cytokine storms in many severely symptomatic covid-19 patients may be rooted in aberrant response to sars-cov-2 by the dysfunctional mcs of mcas rather than normal response by normal mcs. if provable, our conjecture has significant therapeutic and prognostic implications. since december 2019, the covid-19 pandemic, due to the sars-cov-2 coronavirus, has been spreading rapidly throughout many parts of the world, calamitous not only to the personal health and finances of millions but alsolargely due to the infection's high mortality rateto health care systems and societal economic welfare around the globe. approximately 15-20% of covid-19-infected patients suffer a severe course of the acute infection (bulut and kato, 2020; rabec and gonzalez-bermejo, 2020; grasselli et al., 2020) hallmarked by hyperinflammatory cytokine storms causing far more morbidity and mortality than from any direct viral cytotoxicity, and conferring high mortality risk (zhou et al., 2020a) , even 50% or more in some subpopulations (e.g., patients with cardiac injury or requiring continuous renal replacement therapy) (fominskiy et al., 2020; shi et al., 2020; bhatraju et al., 2020; chen et al., 2020) , and requiring hospitalization and, often, mechanical ventilation. the covid-19 cytokine storm is characterized by rapid proliferation and hyperactivation of t cells, macrophages, natural killer cells, and the overproduction of more than 150 inflammatory cytokines and chemical mediators released by immune or nonimmune cells (sun et al., 2020; mangalmurti and hunter, 2020) . among these inflammatory cells, mast cells (mcs) may play an important role because when they recognize viral products, they are activated and synthesize many chemokines and cytokines. in addition, some cytokines secreted by other cells such as t cells, damaged epithelial, and endothelial cells (mukai et al., 2018) , or even by themselves (hermans et al., 2019) , stimulate mc activation. mcs regulate the functions of immune cells such as dendritic cells, monocytes/macrophages, granulocytes, t cells, b cells, and nk cells. they also recruit immune cells to inflamed tissue by secreting chemokines and other mediators which locally increase vascular permeability j o u r n a l p r e -p r o o f (abraham et al., 2010; krystel-whittemore et al., 2016; st john et al., 2011) . the roles of mcs in coronavirus-induced inflammation (kritas et al., 2020; kılınc and kılınc, 2020; theoharides, 2020; zhou et al., 2020) and cytokine storms (theoharides, 2020) have been discussed recently. although mcs can recognize viruses by diverse mechanisms (e.g., toll-like receptor 3 detection of viral double-stranded ribonucleic acid (rna), viral sphingosine-1-phosphate (s1p) binding to s1p receptors, and retinoic acid-induced gene i (rig-i) recognition of uncapped viral rna) (criado et al., 2020) , mcs also express angiotensin converting enzyme 2 (ace2), now appreciated as the principal receptor for sars-cov-2, thus defining a route by which mcs could become hosts for this virus, too. (theoharides, 2020) mcs also express many serine proteases (including tryptase), which are necessary for sars-cov-2 infection. (theoharides, 2020 ) some risk factors for a severe course of covid-19 infection have been identified (e.g., greater age, obesity and/or other chronic pre-existing illness), but specific mechanisms by which such factors would permit more severe infection remain unclear. after the acute infection with covid-19, many then soon manifest a variety of chronic, often inflammatory multisystem illnesses bulut and kato, 2020; scala and pacelli, 2020; troyer et al., 2020; hays, 2020) . another mystery about the covid-19 pandemic is why the infection is mildly symptomatic or even asymptomatic in the majority of those infected but is severely symptomatic, even often lifethreatening, in a sizable minority. in other words, what causes the immune system to suddenly overreact so catastrophically in certain covid-19 patients while remaining properly regulated in the majority? another important question regards the etiology of chronic post-covid-19 illnesses. although solid data on which a proof can be based are not yet available, we j o u r n a l p r e -p r o o f summarize the evidence suggesting that mast cell activation disease, the majority of which is constituted by the prevalent, but only recently recognized, mast cell activation syndrome (mcas), fits very well with these enigmatic findings. we offer a potentially important conjecture, spurred by (1) our familiarity (across several thousand cases over the last dozen years) with mcas (presenting principally as a chronic multisystem polymorbidity of general mc-mediator-driven themes of inflammation ± allergictype issues (afrin et al., 2016a; afrin et al., 2020) ) and (2) our theory that covid-19 inflammatory illnesses may be due to abnormal hyperactivation by sars-cov-2 of the dysfunctional portion of the population of the mutated mcs underlying primary mcas as opposed to normal activation of normal mcs by the virus. primary mcas has been thought by some to underlie, to at least some extent, many of the risk factors identified thus far for severe covid-19 infection (afrin et al., 2016b) . also, it is the natural history of mcas to permanently escalate its baseline level of dysfunction of the affected mcs shortly following a major stressor (likely due to acquisition, due to complex interactions between epigenetic aberrancies and the stressor's induced cytokine storm, of additional mutations by the mutated stem cells from which the mutated/dysfunctional mcs are derived) (molderings, 2015; haenisch et al., 2014; molderings, 2016; altmüller et al., 2017; haenisch et al., 2012; molderings et al., 2010; molderings et al., 2007) . as such, the assortment of (generally inflammatory) post-covid-19 illnesses seen in many covid-19 patients would be a natural course for mcas. in fact, covid-19 would be far from the first infection for which postinfectious chronic multisystem inflammatory illness increasingly is coming to be suspected to be j o u r n a l p r e -p r o o f rooted in (initiation of, or more likely escalation of pre-existing) mcas (e.g., epstein-barr virus infection, tick-borne infections) rather than chronic active infection (afrin, 2016b , kempuraj et al., 2020 . again, since mcas is a chronic multisystem inflammatory disease (with intermittent acute flares) if it is nothing else, it even is possible that at least some of the patients previously thought to have suffered repeat bouts of covid-19 infection might in truth have suffered only an initial bout of infection followed some time later by symptomatic flaring of escalated mcas (e.g., fatigue, myalgias). of further interest, estimates of mcas prevalence (17%, at least in the first world (molderings et al., 2013) ) are closely concordant with estimates of prevalence of severe covid-19 infection. mcs, present in all vascularized tissues but dominantly at the environmental interfaces and in vessel walls (akin and metcalfe, 2004) , are activated by the sars-cov-2 coronavirus which causes covid-19 infection (kritas et al., 2020; theoharides, 2020; zhou et al., 2020) , leading to mc activation and resulting release of various subsets of the mc's >1000 potent multi-action mediators (ibelgaufts, 2020) (including biogenic amines (e.g., histamine), proteases (e.g., tryptase and chymase), cytokines (e.g., interleukins and tnf-α), eicosanoids (e.g., prostaglandins and leukotrienes), heparin, and growth factors) increasingly thought to play a key role in driving the hyperinflammation of severe covid-19 illness (kempuraj et al., 2020; valent et al., 2020) . a significant number of fatal courses of covid-19 infection are due to cardiovascular complications such as pulmonary embolism, thromboembolism, sepsis, and multi-organ failure. it has been shown that mcs play a significant role in promoting thrombotic diseases and j o u r n a l p r e -p r o o f complications; it also has been shown that stabilizing mcs helps prevent fatal sepsis (ramos et al., 2010) . as another example, neuropsychiatric disease appears common in both mcas (afrin et al., 2015) and in covid-19 illness (romero-sánchez et al., 2020) , and though the acute and subacute neurological disease is thought to be due principally to inflammation-induced coagulation, we conjecture that chronic neuropsychiatric symptoms may be due more to escalated (and likely pre-existing) mcas. additionally, some of the drugs or drug classes at least preliminarily shown helpful in modulating the severity of covid-19 infection (e.g., famotidine (freedberg et al., 2020) , aspirin (viecca et al., 2020) ), and for which anti-viral actions seem extremely unlikely, have actions which include inhibiting mc activation or antagonizing released mc mediators. other drugs or drug classes, too, with activity against mcs or their released mediators have been proposed for, or are actively in, trials against covid-19 infection, too [e.g., cromolyn (sestili and stocchi, 2020; sepay et al., 2020; gigante et al., 2020) , flavonoids (theoharides, 2020) , leukotriene inhibitors (almerie and kerrigan, 2020), janus kinase (jak) inhibitors (goker and biray, 2020; seif et al., 2020; luo et al., 2020; spinelli et al., 2020; meyer et al., 2020) , dexamethasone (meyer et al., 2020; recovery collaborative group, 2020) , low-dose naltrexone (sims, 2020) , quercetin (onal, 2020; colunga biancatelli, 2020) , and ascorbic acid (colunga biancatelli, 2020) ]. mcas remains a relatively unrecognized entity in spite of its great prevalence, which likely has been "camouflaged" by its extreme heterogeneity of clinical presentation (afrin et al., 2016a; afrin et al., 2017) , as driven by its underlying extreme mutational heterogeneity. although the mcas in some patients may be purely secondary to another process (e.g., autoimmunity or cancer), mcas clearly is a primary disease in the few in whom it is presently possible to (table 1) . another confounding issue is that many mcas patients who have been undiagnosed for decades ultimately minimize their problems, sometimes deceivingly declaring themselves as "healthy," thus perhaps accounting for at least some of the many severe covid-19 patients described as "healthy" prior to infection. provocatively, in our own mcas patients (i.e., patients already diagnosed and treated, and thus already with at least partial control over their mcas; note many of these patients had long suffered severe courses of mcas prior to diagnosis and having it brought under at least partial control with treatment) who have come to suffer covid-19 infection, none of them have suffered a severe course of the infection (i.e., none have required mechanical ventilation, let alone died), and we conjecture it is precisely because j o u r n a l p r e -p r o o f their dysfunctional mcs were already under at least partial control throughout the acute infection that they have not suffered severe courses, though their mcas still places them at increased risk for developing post-infectious illness (figure 1 ). based on current knowledge, infection causes mild to moderate symptoms in the majority of patients. however, these early data also suggest that even if symptoms are just "mild to moderate" during the acute infection, fibrotic lung damage develops in some, potentially leading to long-term complications for a subset of patients (spagnolo et al., 2020; leask, 2020; lechowicz et al., 2020; george et al., 2020) . it is well known that over-activated mast cells play a crucial role in the development of fibrotic conditions. given that up to 17% of the population is generally pre-disposed to develop syndromes and diseases related to mc activation (molderings et al., 2013) , it is conceivable that people with this predisposition might have increased risk for developing the chronic respiratory, neurologic, or other illnesses increasingly being seen following acute covid-19 illness. (zhou et al., 2020) . we theorize that initiation of mcas-targeted therapy (e.g., inexpensive, safe histamine h1 and h2 receptor antagonists) immediately upon recognition or suspicion of onset of covid-19 illness might mitigate the severity of the illness. the impact on reducing hospitalizations, morbidity, and mortality warrants investigation. we also recommend evaluation for mcas in patients who develop chronic post-covid-19 illnesses. j o u r n a l p r e -p r o o f 13 the fact that mcs normally activate in response to infection precludes diagnostic testing for mcas (i.e., testing for elevated levels in blood and urine of mediators relatively specific to the mc, such as tryptase, heparin, histamine and derivatives, prostaglandin d2 and derivatives (afrin et al., 2020; afrin and molderings, 2014) ) during acute covid-19 infection. however, the potential personal and societal implications of our conjecture are of sufficient magnitude that we nevertheless recommend rapid formal investigation. such investigation should include, at a bare minimum, a pilot clinical trial empirically initiating mcas-targeted therapy in patients newly presenting with suspected covid-19 illness and in whom careful history-taking (regardless of the initially asserted state of prior health) reveals chronic inflammatory and/or allergic issues suspicious for mcas. initial empiric mcas-targeted therapy could include at least histamine h1 and h2 receptor antagonists. note most mcas-targeted therapies are sufficiently safe to make their empiric initiation reasonable. the signaling networks in all inflammatory diseases are extremely complex, and other inflammatory cells besides mcs inescapably are involved in generating the hyperinflammation of covid-19 infection (e.g., the extreme hyperferritinemia seen in some cases might easily be a macrophage activation syndrome or secondary hemophagocytic lymphohistiocytosis sparked by a covid-19-driven escalation of mcas more so than direct virus-driven macrophage activation given that hyperferritinemia is certainly not seen in all patients with severe covid-19 infection (gómez-pastora et al., 2020; ruscitti et al., 2020; ruan et al., 2020; mehta et al., 2020) ). however, we feel the clinical patterns seen thus far in the covid-19 population suggest mcas (likely pre-existing, at that) to be the root issue in many, perhaps even most, of those suffering sciences, ltd. all authors disclaim any financial conflicts of interest. all authors report they had full access to all of the text in this submission and take responsibility for the integrity of any factual statements and analysis. this work has not been presented previously in any other form or venue. no funding or other support was received for this work from any source. no human subjects were involved in this work, and as such, ethical approval was not required for the development of this article. j o u r n a l p r e -p r o o f mast cell-orchestrated immunity to pathogens a concise, practical guide to diagnostic assessment for mast cell activation disease mast cell activation disease: an underappreciated cause of neurologic and psychiatric symptoms and diseases often seen, rarely recognized: mast cell activation disease -a guide to diagnosis and therapeutic options mast cell activation disease and the modern epidemic of chronic inflammatory disease mast cell regulatory gene variants are common in mast cell activation syndrome characterization of mast cell activation syndrome diagnosis of mast cell activation syndrome: a global "consensus-2 the biology of kit in disease and the application of pharmacogenetics the association between obesity and poor outcome after covid-19 indicates a potential therapeutic role for montelukast mutational profiling in the peripheral blood leukocytes of patients with systemic mast cell activation syndrome using next-generation sequencing covid-19 in critically ill patients in the seattle region -case series epidemiology of covid-19 clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study quercetin and vitamin c: an experimental, synergistic therapy for the prevention and treatment of sars-cov-2 related disease (covid-19) what the physicians should know about mast cells, dendritic cells, urticaria, and omalizumab during covid-19 or asymptomatic infections due to sars-cov-2? 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hijaking sars-cov-2? the potential role of jak inhibitors in the management of covid-19 immune surveillance by mast cells during dengue infection promotes natural killer (nk) and nkt-cell recruitment and viral clearance cytokine storm intervention in the early stages of covid-19 pneumonia covid-19, pulmonary mast cells, cytokine storms, and beneficial actions of luteolin are we facing a crashing wave of neuropsychiatric sequelae of covid-19? neuropsychiatric symptoms and potential immunologic mechanisms risk and management of patients with mastocytosis and mcas in the sars-cov-2 (covid-19) pandemic: expert opinions enhanced platelet inhibition treatment improves hypoxemia in patients with severe covid-19 and hypercoagulability. a case j o u r n a l p r e -p r o o f control, proof of concept study unique epidemiological and clinical features of the emerging 2019 novel coronavirus pneumonia (covid-19) implicate special control measures clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan, china: a retrospective cohort study heightened innate immune responses in the respiratory tract of covid-19 patients key: cord-320902-1hfxju5f authors: filocamo, giovanni; mangioni, davide; tagliabue, paola; aliberti, stefano; costantino, giorgio; minoia, francesca; bandera, alessandra title: use of anakinra in severe covid-19: a case report date: 2020-05-11 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.026 sha: doc_id: 320902 cord_uid: 1hfxju5f abstract coronavirus disease 19 is a global healthcare emergency with high lethality rate. relevant inflammatory cytokine storm is associated with severity of disease and il1 inhibition is a cornerstone treatment for hyperinflammatory diseases. we present here the case of a patient with critical covid-19 successfully treated with il-1 receptor antagonist (anakinra). in december 2019, severe acute respiratory syndrome (sars) coronavirus 2 (sarswas firstly discovered in wuhan, china. since then, coronavirus disease 19 (covid-19) has risen to a global healthcare emergency, starting in late february 2020 in northern italy and rapidly becoming pandemic. the spectrum of symptomatic sars-cov-2 infection ranges from mild to critical. while the former accounts for 80% of cases, severe disease with acute respiratory distress syndrome (ards) and critical disease with respiratory failure and/or multiple organ dysfunction are diagnosed in 15-30% and 5% of covid-19 patients, respectively (1). in the first month of covid-19 outbreak in northern italy, intensive care unit (icu) admission represented 12% of all covid-19 patients and 16% of those hospitalized (2) . overall, covid-19 estimated case fatality rate ranges from 2.3% in china to 7.2% in italy (3). however, in china's virus pandemic epicentre during the early stage of covid-19 outbreak, the in-hospital overall lethality rate was higher (28%), and rose up to 62-97% in severely-ill patients requiring mechanical ventilation. (4) . as of march 25 2020, in lombardy, italy, 1591 patients were admitted in icus, of them, 405 (26%) had died in icu, 256 (16%) had been discharged from the icu, while 920 patients (58%) were still in the icu the il-1 receptor antagonist (anakinra) is a cornerstone treatment for hyperinflammatory conditions such as still's disease, and has been shown to be highly effective in the treatment of cytokine storm syndromes, including macrophage activation syndrome and cytokine release syndrome (9). anakinra has a very safe profile and high dosages have been used even in patients with severe viral infection (ebv, h1n1 and ebola) (10). we present here the case of a patient with critical covid-19 successfully treated with anakinra. on february 28 th , 2020 an otherwise healthy 50 year-old man was admitted to the local hospital in crema, lombardy because of fever and dyspnea. infection with sars-cov-2 was confirmed by rt-pcr on nasopharyngeal swab and chest computerized tomography scan showed bilateral ground glass opacities. the patient was put on non-invasive ventilation and antiviral therapy with lopinavir/ritonavir plus hydroxychloroquine was started. at day 3, his conditions worsened requiring icu admission at our hospital for invasive mechanical ventilation and hemodynamic support. on icu admission, the ratio of arterial oxygen partial pressure to fractional inspired oxygen (pao2/fio2) was 160 on pressure control ventilation, with positive end expiratory pressure (peep) 12 and fio2 50%. high levels of acute phase reactants and progressive liver cholestatic injury were observed (table 1) . hepatic involvement with liver enzymes higher more than five-folds their upper limits contraindicated treatment with remdesivir or tocilizumab. at day 10, considering the patient's critical conditions (pao2/fio2 85, volume control ventilation peep 14 fio2 50%) and the hyperferritinemic inflammatory status with ferritin levels more than 3000 ng/ml, use of off-label anakinra was considered and started with the following dosage schedule: 200mg intravenously followed by 100 mg every 6 hours subcutaneously. lopinavir/ritonavir and hydroxychloroquine were interrupted and no other immunosuppressive or immunomodulatory drug, including glucocorticoids or immunoglobulins, was started. in the next 72 hours, a sharp reduction of inflammatory markers and ferritin, an increase in lymphocyte count and a significant reduction of liver enzymes were ob(table 1 ). respiratory parameters improved by day 13 (pao2/fio2 270, pressure control ventilation peep 10 fio2 30%), followed by a favourable radiographic evolution. at day 18 the patient was discharged from the icu. in the following days, respiratory function progressively improved. on day 21, 4 days after icu discharge, the patient became febrile with increase in c-reactive protein levels and no alteration in ferritin levels. considering the persistent improvement in respiratory function and on suspicion of central venous catheter-related bacteremia, anakinra was stopped. intravenous catheter was removed and empiric antibiotic treatment started with vancomycin plus piperacillin/tazobactam, modified 2 days later to cefazolin according to the identification of methicillin-sensitive staphylococcus aureus in blood culture. a complete and prompt response to antibiotic treatment was observed with normalization of acute phase reactants. patient was discharged from the hospital at day 29 in healthy conditions and normal oxygen saturation on room air. to our knowledge, this is the first report of a critical case of covid-19 effectively treated with anakinra. current management of covid-19 is supportive, as respiratory failure from ards is the leading cause of mortality. vaccines and approved targeted therapies for sars-cov-2 infection are still lacking and a multitude of compounds are now under investigation . the need to urgently identify an effective approach to manage covid-19 led to the testing of existing antiviral drugs commonly used for other viral infections (i.e., interferon, ribavirin, and lopinavir-ritonavir), at present with controversial results (11) . remdesevir is a promising novel nucleotide analogue with in vitro activity against sars-cov-2 and proved activity against sars-cov-1 and mers-cov both in vitro and in animal studies (12) . recently a cytokine storm resembling secondary haemophagocytic lymphohistiocytosis (shlh) has been suggested to drive a later hyperinflammatory stage of covid-19, with a decisive role in poor prognosis (13) . shlh is a hyperinflammatory syndrome characterised by lifethreatening hypercytokinaemia leading to multiorgan failure. a cytokine profile resembling shlh, characterized by increased levels of il-2, il-7, granulocyte-colony stimulating factor, inf-γ, cxcl10, monocyte chemoattractant protein 1, macrophage inflammatory protein 1-α, and tnfα was described in severe covid-19 (13) . predictors of mortality from a retrospective, multicentre study of 190 confirmed covid-19 cases in wuhan, china, included elevated ferritin (mean 1435·3 mcg/l in non-survivors vs 503·2 mcg/l in survivors) and il-6 levels (5), suggesting that higher mortality rates may be associated with a virally driven hyperinflammation. the possible role of anti-cytokine treatment with il-6 inhibitor (tocilizumab) in respiratory failure associated to covid-19 has been recently proposed (14) . in inflammatory cytokine storms, il-1 is a key effector and its role in promoting pro-inflammatory cytokines, including il-6, is well known (15) . indeed, il-1 inhibitor anakinra has shown to be highly effective in the treatment of cytokine storm syndromes (15) and has already been proven safe in patients with shlh associated to viral infections such as ebv, h1n1 and ebola (10). its short half-life makes it a widely drug to be use in clinical practice also in critically ill patients, in the eventuality of overcoming situations in which a prompt treatment interruption is required such as bacteraemia as described above. this first report suggests that in the cytokine storm occurring during severe covid-19, il1 inhibition may represent a safe and promising strategy to reduce inflammation preventing multi-organ dysfunction and an appropriate tailored treatment strategy is crucial. further larger cohort observations are needed to confirm the possible association with positive clinical outcomes. to date, may the 5th 2020, 12 clinical trials on anakinra in covid-19 patients are registered on clinicaltrials.gov, 7 of them recruiting patients. these ongoing studies will provide key information on safety and efficacy of anakinra in the hyperinflammatory response to sars-cov-2. characteristics of and important lessons from the coronavirus disease 2019 (covid-19) outbreak in china: summary of a report of 72 314 cases from the chinese center for disease control and prevention critical care utilization for the covid-19 outbreak in lombardy, italy: early experience and forecast during an emergency response case-fatality rate and characteristics of patients dying in relation to covid-19 in italy clinical course and outcomes of critically ill patients with sars-cov-2 pneumonia in wuhan, china: a single-centered, retrospective, observational study baseline characteristics and outcomes of 1591 patients infected with sars-cov-2 admitted to icus of the lombardy region clinical characteristics of coronavirus disease 2019 in china pathogenic human coronavirus infections: causes and consequences of cytokine storm and immunopathology a trial of lopinavir-ritonavir in adults hospitalized with severe covid-19 comparative therapeutic efficacy of remdesivir and combination lopinavir, ritonavir, and interferon beta against mers-cov clinical features of patients infected with 2019 novel coronavirus in wuhan, china effective treatment of severe covid-19 patients with tocilizumab treating inflammation by blocking interleukin-1 in a broad spectrum of diseases key: cord-328459-nmd81sue authors: dioscoridi, lorenzo; carrisi, chiara title: covid-19 exposure risk for family members of healthcare workers: an observational study date: 2020-07-04 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.106 sha: doc_id: 328459 cord_uid: nmd81sue abstract background many papers considered the exposure risk to covid-19 of general population and healthcare workers (hw). however, no available papers discussed the risk of exposure of family members (fm) of hws. aims the present study collected the data of sars-cov-2 positive fm of hws using serological rapid igm/igg tests (srt) compared with positive hws at srt and serological quantitative igg test (sqt). methods the study was conducted from 2nd to 31th may 2020. 38 hws were tested by both srt and sqt; 81 fms were screened using srt. descriptive statistical analyses were used to summarize the data. results of the 38 hws, 2 (5,3%) showed igg line at srt, confirmed by sqt. 32 hws decided self-isolation from the family during sars-cov-2 spreading. out of 81 fms, 26 (32,1%) were found igg positive at srt. 11 (42%) of them had symptoms typical for covid-19 in the study period. in two families, the hws were the only negative case. conclusions general population’s exposure to covid-19 was less controlled than hws’ one. hws experienced lower infection’s rate than their families and did not represented a risk of transmission for relatives. many papers studied covid-19 transmission in family's clusters (lebow jl, 2020 generally, children were not infected. on the basis of these papers, a general concern of healthcare j o u r n a l p r e -p r o o f workers (hw) for their family came up. many hws decided to isolate themselves from their families to reduce the risk of transmission. however, no studies focused on families of hws and sars-cov-2 transmission. this is an observational prospective study. the key element of our study was to assess the total number of family members (fm) of hws positive to sars-cov-2 infection and the number of positive hws working in a covid-19 hospital. hws were tested by both quantitative igg serological test (sqt) during the first week of the study and igm/igg serological rapid test (srt) during the first week and the last week of the study at a constant interval of 4 weeks to calculate the total number of positive cases. srt were performed on fms during the last week of the study. the srt studied both igg and igm with a declared sensitivity of 100% for igg and 85% for igm sqt used in the study was elisa test researching igg anti-s1/anti-s2 for sars-cov-2, available and validated for hws screening in the region of the study (lombardia, italy). study population derived from a high-volume covid-19 hospital of milan, italy. the study period was from the 2 nd to the 31 th may 2020 and the follow-up included the whole study period for hws and fms. in-hospital infection control measures and personal protective equipment (ppe) use were in line with national and international recommendations. all the hws and fms accepted voluntarily to take part in the study. fms were first-degree relatives and/or higher degree ones living in the same house of hws. all the participants were informed about the study and signed an informed consent. for both hws and fms, exposure to covid-19 cases, onset of suspicious symptoms (also before the study period since the 1 st february 2020), photos of the serological tests after 10 minutes, serological tests' platforms, past medical history, drugs and clinical course were registered. all the data were collected in excel database, all the srt platforms were collected and sqt reports were available on our hospital system. descriptive statistical analyses were used to summarize the data. continuous variables with normal distribution were defined as mean and standard deviation. the study size was determined by the number of volunteers in hw's group. all the 38 hws and the 81 corresponding fms accepted to take part in the study and were included according to eligibility criteria. the outcomes were: 1) calculate the number of fms positive to srt for sars-cov-2 infection; 2) calculate the number of hws positive to srt and sqt. the bias of the study included incorrect performance of srt, low sensitivity of srt, confounding factors (drugs, comorbidities, early exposure), use of qualitative tests and interpersonal variability. perform of both tests on hws and inclusion of data on drugs, past medical history of both groups aimed to eventually identify any confounding factor. no subgroup was considered in the present study. study period lasted 29 days (2 nd -31 th may 2020). 38 hws accepted to participate in the study and were included on the base of the eligibility criteria (m 10, f 28, mean age: 4718 y.o.; 9 physicians, 22 nurses and 7 social health professionals). two of the three old fms did physiatry rehabilitation at extended care units. in two families, the hw was the only negative member of the family. youngs and infants were found all negative in the present study. 11 (42%) out of twenty-six cases of igg positive serological tested relatives had respiratory symptoms, fever and/or diarrhea. in all the reported cases the symptoms did not require hospitalization. we identified as potential confounding factors the presence of dubious and not well-demarcated igg line in srt. however, sqt confirmed negative results in these cases. the main limits of the study were the heterogeneity of the fm group and the lack of comparison between srt and sqt in the group of relatives. the study presented the data of covid-19 spreading in hws and their families. a first interesting finding is the high number of relatives positive to sars-cov-2 infection and the lack of correlation between this data and the infected hws. the only two igg positive hws were self-isolated and did not have any contact with their family members during the study period. one possible explanation can be that many hws were false negative to srt and sqt, but this is an unlikely hypothesis because similar results were obtained by both tests and were confirmed at different times. thus, another hypothesis could be that fms had a lower availability of ppe and were exposed to many undiagnosed cases, especially before the lock-down in italy. our study reported all negative young and infant relatives, also in presence of strict and direct contacts in conclusions, our study broke the common thought that hws spread sars-cov-2 infection; according to the found data, hws experienced lesser infection rate than their families and did not represented a major risk of transmission for relatives. the present study was self-founded by santagostino medical center, milan, italy. j o u r n a l p r e -p r o o f family in the age of covid-19 a covid-19 transmission within a family cluster by presymptomatic infectors in china the laboratory diagnosis of covid-19 infection: current issues and challenges epidemiological and initial clinical characteristics of patients with family aggregation of covid-19 the authors declare that they have no conflict of interest. all procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 helsinki declaration and its later amendments or comparable ethical standards. informed consent was obtained from all individual participants included in the study. key: cord-325325-xw7627x9 authors: skeik, nedaa; jabr, fadi i. title: influenza viruses and the evolution of avian influenza virus h5n1 date: 2007-10-02 journal: int j infect dis doi: 10.1016/j.ijid.2007.07.002 sha: doc_id: 325325 cord_uid: xw7627x9 although small in size and simple in structure, influenza viruses are sophisticated organisms with highly mutagenic genomes and wide antigenic diversity. they are species-specific organisms. mutation and reassortment have resulted in newer viruses such as h5n1, with new resistance against anti-viral medications, and this might lead to the emergence of a fully transmissible strain, as occurred in the 1957 and 1968 pandemics. influenza viruses are no longer just a cause of self-limited upper respiratory tract infections; the h5n1 avian influenza virus can cause severe human infection with a mortality rate exceeding 50%. the case death rate of h5n1 avian influenza infection is 20 times higher than that of the 1918 infection (50% versus 2.5%), which killed 675 000 people in the usa and almost 40 million people worldwide. while the clock is still ticking towards what seems to be inevitable pandemic influenza, on april 17, 2007 the u.s. food and drug administration (fda) approved the first vaccine against the avian influenza virus h5n1 for humans at high risk. however, more research is needed to develop a more effective and affordable vaccine that can be given at lower doses. summary although small in size and simple in structure, influenza viruses are sophisticated organisms with highly mutagenic genomes and wide antigenic diversity. they are species-specific organisms. mutation and reassortment have resulted in newer viruses such as h5n1, with new resistance against anti-viral medications, and this might lead to the emergence of a fully transmissible strain, as occurred in the 1957 and 1968 pandemics. influenza viruses are no longer just a cause of self-limited upper respiratory tract infections; the h5n1 avian influenza virus can cause severe human infection with a mortality rate exceeding 50%. the case death rate of h5n1 avian influenza infection is 20 times higher than that of the 1918 infection (50% versus 2.5%), which killed 675 000 people in the usa and almost 40 million people worldwide. while the clock is still ticking towards what seems to be inevitable pandemic influenza, on april 17, 2007 the u.s. food and drug administration (fda) approved the first vaccine against the avian influenza virus h5n1 for humans at high risk. however, more research is needed to develop a more effective and affordable vaccine that can be given at lower doses. # 2007 international society for infectious diseases. published by elsevier ltd. all rights reserved. antigenic drift is a relatively minor antigenic change that occurs frequently within the ha or na of the virus, and is usually responsible for epidemic disease. 5, 6 antigenic shift brings up new viruses with different ha or na antigens. this can be achieved by mutation or genetic reassortment (two different influenza virus strains swap their genes giving rise to a hybrid strain), which usually leads to pandemic disease. 7 the 1918 influenza pandemic was caused by the h1n1 subtype that mutated from a purely avian virus. it was the worst pandemic by far. it killed at least 40 million people worldwide, including 675 000 people in the usa. the average life expectancy in the usa decreased by more than 10 years at that time. [8] [9] [10] [11] the 1957 pandemic was caused by the h2n2 subtype, a product of genetic reassortment in hosts infected with both an avian and human influenza virus. it killed about 70 000 people in the usa. [12] [13] [14] the 1968 pandemic was caused by the h3n2 subtype, a product of genetic reassortment. it killed approximately 34 000 people in the usa. 14 avian influenza is a contagious disease of animals caused by viruses that normally infect only birds, and less commonly, pigs. with the fact that both human and mammalian receptors are present in different proportions in tissues of both species, the bird influenza virus may infect humans. when mutations or reassortments occur, this could lead to the emergence of a fully transmissible strain, as in the 1957 and 1968 pandemics. finally, they can transmit not only to humans but also to other mammals. 15 in birds, the low pathogenic form causes only mild symptoms such as decreased egg production. the high pathogenic form can affect multiple organs and the mortality rate can reach 100%, often within 48 hours. the presence or absence of symptoms and their severity caused by low pathogenic viruses depend on the type of bird species affected. the same holds for the highly pathogenic ones: in wild and domestic ducks they can be asymptomatic, whereas they are lethal in terrestrial birds. 15 the first clinical respiratory illness of h5n1 avian influenza occurred in hong kong in 1997, when 18 human cases were reported during a poultry outbreak. it broke the species barrier to infect humans, cats, and tigers. [16] [17] [18] so far it has affected many countries in asia, africa, and europe. according to the cases reported to the world health organization (who) appearing on the who website on june 29, 2007, the h5n1 virus has already infected 317 humans and has killed 191 patients worldwide, with a mortality rate exceeding 50%. 19 avian influenza h5n1 also affects domesticated poultry, including chickens, ducks, and turkeys. the contribution of migratory birds like wild ducks, geese, swans, and hawks (saudi arabia) to the spread of the h5n1 virus from asia to europe and africa is still controversial, since basically all wild birds positive for h5n1 virus have been found dead or very sick, thus unlikely to have been able to fly over long distances. at the same time, more evidence supports the role of the international illegal poultry trade. it is possible that this trade contributed to the 2006 h5n1 outbreak in a large commercial farm in kaduna state in the northern part of nigeria. on the other hand, the country is known to lie along a flight route for birds migrating from central asia. the birds shed the virus in their saliva, nasal secretions, and feces. infection can spread among birds by contact with infected birds or with their excretions. people can get infected by direct or close contact with infected poultry or surfaces contaminated with secretions and excretions from the infected birds. human exposure occurs most often during slaughtering, de-feathering, butchering, or preparation for cooking. raw poultry or eggs can also transmit the disease. there are no reported cases through properly cooked poultry. 15, 20 human-to-human transmission was suggested in a family in thailand, when an 11-year-old girl who had been in contact with an infected bird, and her mother who had provided her with nursing care, both died of the avian influenza. the girl's aunt, who had also had close contact with the girl, survived the infection after treatment with oseltamivir. h5n1 was confirmed in the mother and the aunt. 21, 22 recently there have been fears of other human-to-human transmission cases after seven family members died of the avian influenza in indonesia. who confirmed that partial human-to-human transmission occurred. 20 other potential modes of transmission of h5n1 virus include contamination of hands from infected fomites and exposure to untreated poultry feces used as fertilizers. further possible but not proven modes of transmission are oral ingestion of contaminated water during swimming and direct intranasal or conjunctival inoculation during exposure to water. 23 the virulence of the avian influenza viruses in mammals is not well understood. as opposed to the earlier h5 viruses, the more recently circulating h5 viruses appear to be more pathogenic in mammals and birds. this is a feature that may precede the emergence of reassorted h5 strains with pandemic potential. 17, 24 although virulence determinants are polygenic traits, the possible major contributing factor is the hemagglutinin molecule. the acquisition of a multibasic amino acid sequence at the cleavage site of a hemagglutinin belonging to the h5 or h7 subtypes enables its widespread cleavage by ubiquitous tissue proteases, resulting in multi-organ infection and high pathogenicity. 25, 26 h5n1 viruses are relatively resistant to host antiviral cytokines, which leads to the production of high levels of cytokines and an excessive pro-inflammatory response causing tissue injury. 27, 28 this suggests that the severity of human h5n1 infection may be related to the excessive pro-inflammatory responses that exacerbate tissue injury. 23, 29 autopsies of current human cases of h5n1 influenza have revealed necrotizing hemorrhagic pneumonia, similar to that found in the 1918 influenza cases. like the 1918 virus, h5n1 is associated with unusually high death rates in humans; in fact the case death rate is 20 times higher than that of the 1918 virus (50% vs. 2.5%). 30 continuous evolution of the h5n1 virus has been suggested by changes in the internal gene constellation, expanded host range, increased pathogenicity, and greater environmental stability. 31, 32 symptoms and signs according to one study, symptoms of h5n1 infection include typical influenza-like symptoms: fever (100%), cough and sore throat (67%), myalgias (30%), pneumonia (58%), diarrhea and vomiting (50%), and congestion of the conjunctiva (0%). laboratory findings include elevated serum aminotransferases and pancytopenias. 23, 33 complications include acute respiratory distress syndrome (ards), pulmonary hemorrhage, myocarditis, pericarditis, encephalitis, multi-organ failure with renal dysfunction, and sepsis. most deaths have been related to respiratory failure. 23 the spectrum of disease is wide. two children from the same family in vietnam presented with diarrhea and encephalopathy, without any signs of respiratory compromise. 34, 35 the incubation period for h5n1 may be longer than other known human influenza viruses. 23 in 1997, most cases occurred within two to four days after exposure, while reports of cases from 2004 suggest that longer intervals of up to eight days may be possible. 16, 36 diagnosis diagnosis can be made with clinical findings, plus recent history of exposure to dead or ill poultry, and can be confirmed with serologic tests. travel history is also very important. rapid antigenic testing kits are not able to subtype influenza a, and the standard serologic test (ha inhibition test) is insensitive. [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] diagnosis can be confirmed by haspecific pcr assay or by viral culture of a nasopharyngeal aspirate obtained within three days of the onset of symptoms. 23 elisa and western blotting are useful for epidemiologic surveillance studies and retrospective diagnosis. 37 radiologic findings include diffuse, multi-focal or patchy infiltrates and segmental or lobar consolidation with air bronchograms. 36 the differential diagnoses of avian influenza include atypical pneumonia, human influenza, respiratory syncytial virus, severe acute respiratory syndrome (sars), and upper respiratory tract infections associated with conjunctivitis (e.g., adenovirus). high-risk individuals, such as patients with a history of travel within 10 days of symptom onset to a country with documented h5n1 avian influenza in poultry and/or humans, and patients who have radiographically confirmed pneumonia, ards, or any other severe respiratory illness for which an alternate etiology has not been established, should be tested. for low-risk individuals, testing should be considered in patients with a history of contact with domestic poultry or with a known or suspected human case in an h5n1-affected country within 10 days of symptom onset, documented fever of 38 8c, and one or more of the following: cough, sore throat, shortness of breath. 23, 36 treatment whenever feasible, while the number of affected persons is small, patients with suspected or proven influenza a (h5n1) infection should be hospitalized in isolation for clinical monitoring, appropriate diagnostic testing, and antiviral therapy. 38 the majority of h5n1 isolates are still sensitive to amantadine. however, more recent viruses isolated in thailand and vietnam have amino acid substitutions within the m2 protein, which confer resistance to amantadine and rimantadine. 39, 40 these viruses are susceptible to the neuraminidase inhibitors in animal models. 41 oseltamivir should be started as soon as possible. in an animal study where mice were inoculated with h5n1 virus isolated from a patient who did not survive the infection, the mice that were treated for eight days with oseltamivir had significantly better survival rates in all dose ranges when compared to animals that were treated for only five days. 39 prior animal studies demonstrated that five days of oseltamivir was effective against another h5n1 variant. 42 thus, treatment dose and duration may vary according to the pathogenicity and virulence of the virus. 39 an oseltamivir-resistant h5n1 strain (his274tyr) has been reported in two cases in vietnam. both patients died of the infection despite early initiation of treatment in one case and proper dosage (75 mg twice daily) in both cases. therefore, the use of higher doses, longer durations of treatment, or combination therapy may deserve further evaluation. 43 improper use of personal stockpiles of oseltamivir may promote resistance and should be strongly discouraged. 44 zanamivir is another neuraminidase inhibitor, and was the first neuraminidase inhibitor to be approved for influenza treatment. it is also recommended for the treatment of h5n1 infection, together with oseltamivir. corticosteroids have been used frequently in treating patients with h5n1 infection with uncertain effects. other agents like peramivir, long-acting topical neuraminidase inhibitors, ribavirin, 45, 46 and possibly interferon alpha, which has both antiviral and immunomodulatory activities, are under investigation. 47 according to a recent report, patients with spanish influenza pneumonia who received influenza-convalescent human blood products may have experienced a clinically important reduction in the risk of death. convalescent human h5n1 plasma could have similar benefits and should be studied in clinical trials. 48 although immunization with human influenza vaccine will not protect against avian influenza strains, it should be considered in poultry workers, and also be given to those traveling to affected areas, two weeks ahead of departure, to prevent co-infection and reassortment. 23 according to centers for disease control and prevention (cdc) and who recommendations, people who live in affected areas should avoid all direct contact with poultry and surfaces contaminated with poultry feces and secretions, should avoid eating undercooked eggs and poultry, should wash hands carefully and frequently, and should seek medical attention if they become ill within 10 days of suspected contact. 15, 20 post-exposure prophylaxis with oseltamivir 75 mg daily for 7 to 10 days should be recommended to household contacts of patients. 23, 49, 50 although the risk of transmission from person influenza viruses and the evolution of avian influenza virus h5n1 to person appears low, quarantining of close contacts to patients for a week after last exposure and monitoring for symptoms may help to reduce transmission rates. 23 if available, negative pressure rooms should be used for patient isolation. healthcare workers should wear n-95 masks (non-oilproof respirators with at least 95% efficiency in filtering particles more than 3 mm in diameter), gloves, long sleeved cuffed gowns, and eye protection when within 3 feet of patients. 51 quarantine and depopulation or culling of affected poultry is the preferred way of eradication. the use of inactivated h5n1 vaccines in chickens is an additional step but should be done with caution. 52 vaccine currently, there is no commercially available vaccine against h5n1 virus. due to safety and technical reasons, and since h5n1 is highly virulent and lethal to eggs, traditional methods of production are not feasible. furthermore, it is impossible to predict whether the currently circulating h5n1 strain will cause the next pandemic. if successfully produced, vaccines would likely be the most important health tools to decrease morbidity, mortality, and the economic effects of pandemic influenza. resistance to oseltamivir makes vaccines even more important. 23, 53 the h5n1 viruses can be divided into clade 1 and clade 2; the latter can be further subdivided into three subclades. these clades and subclades probably differ sufficiently in their antigenic structure to warrant the preparation of different vaccines. studies in ferrets suggest that vaccination against one clade will not protect against infection with another clade, though it will protect against influenza-associated death. 54 a new vaccine prepared from an egg-grown recombinant influenza a virus, composed of the hemagglutinin and neuraminidase genes from a human h5n1 isolate inserted into a laboratory-adapted human influenza a strain, achieved only 54% presumably protective micro-neutralization titers of 1:40 following use of the maximum tested dose (90 mg). this dose is 12 times that of the seasonal influenza vaccine, making mass production untenable with current manufacturing capacity. current seasonal vaccines contain 15 mg ha/ strain/dose. whether this vaccine could induce cross-protection against other h5n1 strains is unclear. furthermore, the death of a chinese woman infected with an h5n1 strain markedly different from those now being used to develop vaccines has recently been reported. [55] [56] [57] studies of different dose levels of vaccines administered with adjuvants like aluminum hydroxide are urgently needed to improve immunogenicity and increase the number of doses available (if lower doses are effective). [57] [58] [59] recently, promising progress has been made in industry-supported research in france and the uk, where the safety and immunogenicity of a monovalent, inactivated split-virion vaccine, derived from a highly pathogenic strain of h5n1 influenza, has been investigated; this vaccine was administered with and without a fixed dose of aluminum hydroxide as an adjuvant. on day 42, 67% of subjects who received the highest dose ha with adjuvant exhibited detectable antibody titers, and 61% had positive ha-inhibition responses. 60 other promising approaches to vaccine development involve dna, adenovirus vectors, and cell manufacturing techniques to increase the speed and capacity of vaccine production. 61, 62 on april 17, 2007, the u.s. food and drug administration (fda) approved a human vaccine against the h5n1 influenza virus, marking the first such approval in the usa. should h5n1 develop the ability to spread readily from person to person, this vaccine may provide early limited protection in the months before a vaccine tailored to the pandemic strain of the virus can be developed and produced. the vaccine will be kept in a federal stockpile and will be made available only through public health officials; it is approved for those aged 18 to 64 years who are at increased risk for h5n1 exposure. 63 for a pandemic to occur, three conditions must be met: a new influenza virus subtype must emerge, this must infect humans and cause serious disease, and finally spread easily among humans. 20 the first two conditions have already been met, and there are new suggestions of human-to-human transmission in thailand and indonesia. however, there is no evidence to-date of the easy human-to-human transmission that is key for a pandemic. [20] [21] [22] [23] with the emergence of influenza virus h5n1, the threat of an influenza pandemic seems to be real and inevitable, but no one can predict when it might happen. according to a study by the congressional budget office, the consequences of a severe pandemic could, in the usa, include 200 million people infected, 90 million clinically ill, and 2 million dead. the study estimated that 30% of all workers would become ill and 2.5% would die, resulting in a decrease in the gross domestic product of 5%. furthermore, 18 to 45 million people would require outpatient care, and the economic cost would total approximately $675 billion. 64 the world is facing the real threat of another influenza pandemic with a virus that has a great pathogenicity and a mortality rate in humans exceeding 50%. despite the high level of technology and ongoing research, at the present time there is no highly effective vaccine against avian influenza h5n1 virus that can be manufactured commercially on a large scale for use at low doses. as is always said, ''a dime of prevention is better than a pound of treatment''. responsibility should be taken at all levels and preventative steps should be implemented immediately. healthcare providers should be up-to-date with the pandemic risk and educate their patients. such information can be found at www.cdc.gov/flu. other sources of information include www.defra.gov.uk, www.fda.gov, www.who.int, and www.eurosurveillance.org. conflict of interest: no conflict of interest to declare. harrison's principles of internal medicine evolution and ecology of influenza a viruses global epidemiology of influenza: past and present influenza virus neuraminidase inhibitors influenza virus antigens and 'antigenic drift analysis of antigenic drift in recently isolated influenza a (h1n1) viruses using monoclonal antibody preparations influenza--a model of an emerging virus disease enhanced virulence of influenza a viruses with the haemagglutinin of the 1918 pandemic virus the genetic archaeology of influenza characterization of the reconstructed 1918 spanish influenza pandemic virus transmissibility of 1918 pandemic influenza the threat of an avian influenza pandemic on the origin of the human influenza subtypes h2n2 and h3n2 avian-to-human transmission of the pb1 gene of influenza a viruses in the 1957 and 1968 pandemics questions and answers about avian influenza (bird flu) and avian influenza a (h5n1) virus clinical features and rapid viral diagnosis of human disease associated with avian influenza a h5n1 virus avian h5n1 influenza in cats avian influenza h5n1 in tigers and leopards cumulative number of confirmed human cases of avian influenza a/(h5n1) reported to who avian influenza frequently asked questions probable person-to-person transmission of avian influenza a (h5n1) transmission of avian influenza viruses to and between humans avian influenza a (h5n1) infection in humans h5n1 influenza: a protean pandemic threat molecular basis for high virulence of hong kong h5n1 influenza a viruses pb2 amino acid at position 627 affects replicative efficiency, but not cell tropism, of hong kong h5n1 influenza a viruses in mice lethal h5n1 influenza viruses escape host anti-viral cytokine responses induction of proinflammatory cytokines in human macrophages by influenza a (h5n1) viruses: a mechanism for the unusual severity of human disease? re-emergence of fatal human influenza a subtype h5n1 disease avian influenza: an emerging pandemic threat avian influenza in hong kong antigenic differences between h5n1 human influenza viruses isolated in 1997 and antibody response in individuals infected with avian influenza a (h5n1) viruses and detection of anti-h5 antibody among household and social contacts fatal avian influenza a (h5n1) in a child presenting with diarrhea followed by coma human disease from influenza a (h5n1) detection of antibody to avian influenza a (h5n1) virus in human serum by using a combination of serologic assays world health organization. who interim guidelines on clinical management of humans infected by influenza a (h5n1) virulence may determine the necessary duration and dosage of oseltamivir treatment for highly pathogenic a/vietnam/1203/04 influenza virus in mice update: influenza activity--united states and worldwide, 2003-04 season, and composition of the 2004-05 influenza vaccine genesis of a highly pathogenic and potentially pandemic h5n1 influenza virus in eastern asia comparison of efficacies of rwj-270201, zanamivir, and oseltamivir against h5n1, h9n2, and other avian influenza viruses oseltamivir resistance in influenza a (h5n1) infection the run on tamiflu--should physicians prescribe on demand? in vitro inhibitory effects of combinations of anti-influenza agents ribavirin aerosol treatment of influenza absence of interferon in lungs from fatal cases of influenza meta-analysis: convalescent blood products for spanish influenza pneumonia: a future h5n1 treatment? management of influenza in households: a prospective, randomized comparison of oseltamivir treatment with or without postexposure prophylaxis effectiveness of oseltamivir in preventing influenza in household contacts: a randomized controlled trial protecting healthcare staff from severe acute respiratory syndrome: filtration capacity of multiple surgical masks preparation of a standardized, efficacious agricultural h5n3 vaccine by reverse genetics confronting the avian influenza threat: vaccine development for a potential pandemic immunization with reverse-genetics-produced h5n1 influenza vaccine protects ferrets against homologous and heterologous challenge safety and immunogenicity of an inactivated subvirion influenza a (h5n1) vaccine lethal avian influenza a (h5n1) infection in a pregnant woman in anhui province, china vaccines against avian influenza--a race against time immunogenicity of a monovalent, aluminum-adjuvanted influenza whole virus vaccine for pandemic use pandemic preparedness: lessons learnt from h2n2 and h9n2 candidate vaccines safety and immunogenicity of an inactivated split-virion influenza a/vietnam/1194/2004 (h5n1) vaccine: phase i randomized trial development of adenoviral-vector-based pandemic influenza vaccine against antigenically distinct human h5n1 strains in mice from lethal virus to life-saving vaccine: developing inactivated vaccines for pandemic influenza fda approves first u.s. vaccine for humans against the avian influenza virus h5n1 a potential influenza pandemic: an update on possible macroeconomic effects and policy issues key: cord-330692-rqwkkfp0 authors: he, daihai; shi, zhao; li, yingke; cao, peihua; gao, daozhou; lou, yijun; yang, lin title: comparing covid-19 and the 1918–19 influenza pandemics in united kingdom date: 2020-06-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.075 sha: doc_id: 330692 cord_uid: rqwkkfp0 abstract we compare the covid-19 pandemic and 1918-19 influenza pandemic in united kingdom. we found that the on-going covid-19 wave of infection matched the major wave of the 1918-19 influenza pandemic surprisingly well, both reached similar magnitude (in term of estimated weekly new infections) and spent the same duration above 5 cases per 1000 inhabitants, for the past two months. we discussed the similar characteristics between these two pandemics. the fast spread and high fatality of the coronavirus disease 2019 (covid-19) remind us of the first pandemic in last century, the 1918-19 influenza pandemic. indeed, the sars-cov-2 and the 1918 a/h1n1 influenza viruses share some common properties.  similar basic reproductive number (r0), ranging from 2 to 4;  similar patterns of viral shedding from infectious patients1 ,2 thus presumably comparable generation intervals; zou et al (2020) reported "our analysis suggested that the viral nucleic acid shedding pattern of patients infected with sars-cov-2 resembles that of patients with influenza and appears different from that seen in patients infected with sars-cov". in particular, covid-19 may have a similar latent period as that of influenza;  comparable dispersion parameter k 3, which controls the variance of the distribution of number of secondary cases caused by a typical primary case. smaller k implies bigger contribution in the total infections from super-spreaders. for instance, 1918 influenza a/h1n1 has a relatively large k (0.94)4 compared with severe acute respiratory syndrome (sars, 0.16) and middle-east respiratory syndrome (mers, 0.26). it was found that that k for covid-19 may be 0. 8 we used the age grouped p&i data and we assume a maximum age of 80. a comparison between the ylls for covid-19 and 1918-19 influenza should be conducted, because yll is the other important indicator of the severity of a pandemic. there are many reasons to compare the current pandemic and the 1918-19 pandemic. we attempted such a preliminary comparison in figure 2 . however, this 'match' is artificial since we choose 5% reporting ratio without strong support. we choose to match the ongoing covid-19 to the fall wave in 1918 due that the summer wave was very minor and obviously not comparable. the population size was 44 million in 1918 and are 59 million in 2020 in e&w. if we assume a 0.5% ifr for covid-19 in 2020 and a 2% infection fatality rate in 1918, we may calculate and compare the infections based on reported deaths which should be more reliable than reported cases. in figure 2b , we showed such a comparison, the 'match' is unexpected. here the 0.5% ifr for covid-19 is a reasonable guess based on serological study in german gangelt8 and observed infection fatality rate in hong kong9 and singapore10 where testing was extensive. furthermore, according to faust and del rio 11, the cfr on the diamond princess cruise outbreak was 0.5% after age standardization. the two matched surprisingly well between week 7 and 16, and above 5 cases per 1000 inhabitants. years of life lost due to pneumonia and influenza between 1911 and 1921 in london, uk sars-cov-2 viral load in upper respiratory specimens of infected patients virological assessment of hospitalized patients with covid-2019 superspreading and the effect of individual variation on disease emergence influenza transmission in households during the 1918 pandemic clustering and superspreading potential of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infections in hong kong mechanistic modelling of the three waves of the 1918 influenza pandemic prioritization of influenza pandemic vaccination to minimize years of life lost assessment of deaths from covid-19 and from seasonal influenza reconstruction of transmission pairs for novel coronavirus disease 2019 (covid-19) in mainland china: estimation of super-spreading events, serial interval, and hazard of infection the effect of public health measures on the 1918 influenza pandemic in us cities inferring the causes of the three waves of the 1918 influenza pandemic in england and wales acknowledgements dh thanks jonathan dushoff, lewi stone and david earn for insightful discussion. we thank international infectious disease data archive (iidda) for influenza data. key: cord-286743-z0e5arlm authors: langer-gould, annette; smith, jessica b.; gonzales, edlin g.; castillo, rhina d.; garza figueroa, judith; ramanathan, anusha; li, bonnie h.; gould, michael k. title: early identification of covid-19 cytokine storm and treatment with anakinra or tocilizumab date: 2020-08-06 journal: int j infect dis doi: 10.1016/j.ijid.2020.07.081 sha: doc_id: 286743 cord_uid: z0e5arlm objective: to examine outcomes among patients who were treated with the targeted anti-cytokine agents, anakinra or tocilizumab, for covid-19 -related cytokine storm (covid19-cs). methods: we conducted a retrospective cohort study of all sars-cov2-rna-positive patients treated with tocilizumab or anakinra in kaiser permanente southern california. local experts developed and implemented criteria to define covid19-cs. all variables were extracted from the electronic health record. results: at tocilizumab initiation (n = 52), 50 (96.2%) were intubated, and only 7 (13.5%) received concomitant corticosteroids. at anakinra initiation (n = 41), 23 (56.1%) were intubated, and all received concomitant corticosteroids. fewer anakinra-treated patients died (n = 9, 22%) and more were extubated/never intubated (n = 26, 63.4%) compared to tocilizumab-treated patients (n = 24, 46.2% dead, n = 22, 42.3% extubated/never intubated). patients who died had more severe sepsis and respiratory failure and met covid-cs laboratory criteria longer (median = 3 days) compared to those extubated/never intubated (median = 1 day). after accounting for differences in disease severity at treatment initiation, this apparent superiority of anakinra over tocilizumab was no longer statistically significant (propensity score-adjusted hazards ratio 0.46, 95% confidence interval 0.18–1.20). conclusions: prompt identification and treatment of covid19-cs prior to intubation may be more important than the specific type of anti-inflammatory treatment. randomized controlled trials of targeted anti-cytokine treatments and corticosteroids should report duration of cytokine storm in addition to clinical severity at randomization. anakinra, a short-acting il-1 receptor antagonist is the preferred treatment for severe forms of cytokine storm for patients with underlying conditions other than covid-19, but its use was not reported for covid-19 patients in china. however, a more recent study from italy (cavalli et al., 2020) (n=29) reported significantly improved respiratory function in 21 (72%) patients 21 days after initiating highdose iv anakinra in patients with moderate-severe ards treated with continuous positive airway pressure (cpap). at kaiser permanente southern california (kpsc), the treatment of covid19-cs has evolved along with this limited evidence base. initially, treatment options for cytokine storm included tocilizumab (without corticosteroids), but not anakinra. subsequently, a shift in practice by clinicians at some of our medical centers aimed to identify early covid19-cs through laboratory abnormalities in patients with increasing o2 requirements and to initiate combined treatment with anakinra and corticosteroids occurred. this was guided by prior institutional experience with treating macrophage activating syndrome (mas) and hemophagocytic lymphohistiocytosis (hlh), which present with similar but not identical manifestations of covid19-cs (jordan et al., 2019) . in this paper, we describe the initial experience with tocilizumab and anakinra for the treatment of patients with covid19-cs at 15 kpsc hospitals in southern california. while treatments were not randomly assigned, the evolution in practices over time provided an opportunity for us to compare the different approaches. our primary aim was to describe clinical outcomes among tocilizumab-or anakinra-treated covid-19 patients, and to examine whether differences in outcomes could be accounted for by covid19-cs severity and/or duration at the time of treatment initiation. we conducted a retrospective cohort study of all sars-cov2-rna-positive patients treated with at least 1 dose of tocilizumab between 3/1/2020-4/13/2020 or anakinra, 4/1-4/30/2020, at one of 15 kpsc j o u r n a l p r e -p r o o f hospitals in southern california. the dates vary because anakinra was not used in our hospitals for covid19-cs in march. outcomes and covariates were abstracted from the complete electronic health records (ehr) until the date of death, or 30 days after last dose. study population. we searched electronic databases to identify kpsc members treated with tocilizumab or anakinra and reviewed the complete ehr to confirm that these drugs were administered to treat covid19-cs. covid19-cs was defined clinically by increasing o2 requirements and bilateral infiltrates on chest x-ray or ct. anakinra dosing and duration was guided on a per-patient basis by a team of experts in immunology and varied based on severity of ards, laboratory abnormalities and renal function. anakinra use was defined as: 1) 5 or more consecutive days of treatment regardless of daily dose (n=35); or 2) at least 1 day of high-dose anakinra (100mg sq every 6 hours; or every 12 hours for those with renal failure) and discontinuation of anakinra due to death (n=3), significant clinical improvement (n=3) or adverse events (n=0). patients were excluded if they received tocilizumab or anakinra for other indications (n=3), or if either drug was ordered but never administered (n=3). in addition, 13 anakinra-treated patients were excluded because the dose and/or duration of treatment were inadequate and not related to adverse events. setting. kpsc is a large pre-paid health care organization that provides comprehensive health care services to over 4.6 million members in southern california. the membership of kpsc is representative of the general southern california population (koebnick et al., 2012) . kpsc uses an integrated ehr system which includes all inpatient and outpatient encounters, laboratory and imaging tests, diagnoses and medications, and demographic and behavioral characteristics. standard protocol approvals, registrations, and patient consents. the study protocol was approved by the kpsc institutional review board (#12396). data collection. data were extracted by manual reviewing the ehr, including onset of dyspnea and other covid-19 symptoms, age, sex, comorbidities, smoking status, tocilizumab and anakinra use, other j o u r n a l p r e -p r o o f treatments rendered for hydroxychloroquine, and/or corticosteroids) , fever (>100.4f), hypotension requiring pressors, dates of admission, intubation, extubation, discharge and/or death. the following variables were abstracted from the ehr at three different time periods, including the time of admission, the date of the first tocilizumab/anakinra dose and seven days post last tocilizumab or first anakinra dose (for those still intubated at the time): pao2/fio2 ratios (p/f ratio) calculated from first morning blood gases; fio2 requirements (for ventilated patients), liters of o2 on nasal cannula (nc); presence, onset and resolution of acute kidney injury (aki, defined as 2-fold increase in serum creatinine), acute kidney failure requiring hemodialysis and chest x-ray and computerized tomography (ct) radiology reports. beginning in april 2020, laboratory tests and absolute counts of lymphocytes and neutrophils obtained throughout the hospitalization were reviewed and classified according to modified hlh/mas diagnostic criteria (jordan et al., 2019) . these covid19-cs laboratory criteria are as follows: 1) ferritin >2000ng/ml and one other abnormal inflammatory marker; or 2) ≥4 abnormal inflammatory markers, including c-reactive protein >70mg/l; ferritin>700ng/ml, d-dimer>1000ng/ml, triglycerides >265mg/dl, ast >59u/l, ldh >300iu/l, lymphopenia <800 cells/ul and neutrophilia >8000cells/ul. due to the relatively large number of missing lab test results at treatment initiation (n=17), the criteria were adapted for the purposes of this study to include patients who had 3 abnormalities when 4 or fewer labs were measured. for patients who did not have 5 or more of these lab tests ordered on the same day, laboratory abnormalities occurring +/-2 days apart were included. covid19-cs was operationally defined based on a combination of these laboratory abnormalities and the clinical criterion of progressive worsening of respiratory status. outcomes of interest included treatment failure (death) and treatment response, defined as avoiding or being liberated from mechanical ventilation. j o u r n a l p r e -p r o o f statistical analyses. the primary purpose of analyses was to describe clinical outcomes among tocilizumab-or anakinra-treated covid-19 patients and to examine whether differences in outcomes could be accounted for by covid19-cs severity and/or duration at the time of treatment initiation (baseline). in addition, we identified potential confounders of the relationship between treatment and outcomes by examining the crude association of baseline co-variates with treatment failure and treatment response. the association between treatment with anakinra or tocilizumab (t0) and the time to death was graphically depicted using kaplan-meier survival curves. a propensity score (ps)-adjusted cox regression model was employed to account for imbalances in multiple baseline characteristics at the time of treatment initiations. the predicted probability of starting anakinra (as opposed to tocilizumab) was modeled using multiple logistic regression. the following covariates were included: age (continuous); sex; comorbidities, diabetes (yes/no), hypertension (yes/no), obesity (body mass index >30, yes/no), ever smoker (yes/no), asthma or copd (yes/no); other sars-cov-2 antiviral treatments, remdesivir (yes/no) or hydroxychloroquine (yes/no); time from symptom onset, onset of dyspnea and admission to first-dose (in days); clinical measures of disease severity each modeled as a single yes/no variable, presence of fever, aki, hypotension, lymphopenia, neutrophilia, lymphopenia and neutrophilia or being intubated at baseline; duration of intubation (days, in tertiles; not intubated=0) and duration of meeting covid19-cs laboratory criteria (days, in tertiles) at baseline. the cox regression model was then adjusted for the propensity score (ps) covariate derived from the logistic regression model. the robust sandwich covariance matrix estimate was used to account for patients who received tocilizumab and anakinra (n=1). the means and standard deviations of normally distributed variables were compared using 2sample t-tests; for variables with non-normal distributions, the wilcoxon rank-sum test was used; and for binary or categorical variables, chi-square with the fisher exact test. statistical significance was set j o u r n a l p r e -p r o o f at p = 0.05. no adjustment for multiple comparisons was made. all statistical analyses were performed using sas version 9.4 (sas institute inc, cary, nc). fifty-two patients received 1-4 doses of tocilizumab and 41 received anakinra, a median of 14 days (iqr 9.5-17 days) and 13 days (iqr 10-18) after symptom onset, respectively. most tocilizumab-treated patients received 1 dose (n=26), 18 received 2 doses, seven received 3 doses, and one received 4 doses. the median duration of anakinra treatment was 9 days (iqr 6-11), and the median cumulative dose was 1500mg (iqr 1200-2400). all patients had bilateral infiltrates on chest x-ray or ct, and all non-intubated patients had increasing supplemental o2 requirements at the time of treatment initiation. table 1 shows the demographic, clinical and laboratory characteristics of tocilizumab and anakinra-treated patients at treatment initiation. more tocilizumab-treated patients were males, but fewer had pre-existing hypertension or were obese compared to anakinra-treated patients. more tocilizumab-treated patients were intubated at the time of treatment initiation, but the duration of intubation and pa02:fio2 ratios among intubated patients treated with tocilizumab were similar compared to those treated with anakinra. only 31 of 52 (59.6%) of tocilizumab-treated patients met full cs laboratory criteria at treatment initiation. eight (15.4%) met clinical but not laboratory criteria for covid19-cs, 3 (5.8%) patients had not been monitored for laboratory indicators of covid19-cs, and 10 (19.2%) had insufficient labs measured (<5) to fulfill the full cs laboratory criteria but did meet modified criteria (3 abnormal labs). in contrast, 37 of 41 (90.2%) of anakinra-treated patients had been monitored (n=37) and all but 1 met full covid-cs laboratory criteria at treatment initiation. more tocilizumabtreated patients had fever, hypotension, aki, neutrophilia and the combination of lymphopenia and neutrophilia compared to anakinra-treated patients. concomitant corticosteroids were used in only 7 tocilizumab-treated patients, although 12 others received rescue treatment with steroids later in their hospital course. in contrast, all anakinratreated patients received concomitant corticosteroids. of the 48 patients who received concomitant corticosteroids, only 2 patients in the anakinra-treated group received more than the maximum recommended daily dose (40mg bid of methylprednisolone or equivalent doses of other corticosteroids). remdesivir treatment was similar between groups (n=20 tocilizumab, n=16 anakinra) while fewer anakinra-treated patients received hydroxychloroquine (n=34) compared to tocilizumab (n=48). figure 1 shows the outcomes among tocilizumab and anakinra-treated patients at the end of follow-up. the median follow-up time from first dose to end of study among patients that survived was longer for tocilizumab (24 days, iqr 20.5-27.0) than anakinra (19 days, iqr 13.5-21.0). the risk of death was lower in the anakinra group (22.0%) than the tocilizumab group (46.2%), and the percentage of anakinra treatment responders was correspondingly higher (63.4% versus 43.2%). among the 18 nonintubated patients at anakinra start, 14 never required intubation, 3 were subsequently intubated (1 extubated and 2 still intubated), and 1 elderly man was not intubated in accordance with his family's wishes and died. of the 23 intubated patients at anakinra initiation, 11 (47.8%) were extubated at last follow-up compared to 20 (40%) of the 50 intubated patients at tocilizumab initiation. compared with patients who were still alive, the patients who died were slightly older, more likely to have pre-existing hypertension or diabetes; more likely to be intubated, have aki, hypotension and more severe ards; and had a longer duration of covid19-cs laboratory abnormalities including neutrophilia at the time of treatment initiation with either drug ( table 2) . those who died all had rising inflammatory markers consistent with worsening covid19-cs at the time of death. lymphopenia and/or neutrophilia resolved following treatment initiation in most patients who survived, but not in those who died. unadjusted analysis indicated a survival advantage with anakinra compared to tocilizumabtreated patients (figure 2) , but after adjustment for multiple baseline imbalances this difference did not reach statistical significance (ps-adjusted hr= 0.46, 95%ci= 0.18-1.20, p=0.11). effective treatments for covid-19 and covid19-cs are needed urgently. in this study, we found that only 42.3% of tocilizumab-treated patients and 63.4% of those treated with anakinra responded favorably to treatment. our health system's initial experience with tocilizumab early in california's covid-19 outbreak was less favorable than that previously reported in the case series from china (xu et al., 2020) . this disappointing tocilizumab experience led to a shift in practice to identify covid19-cs earlier in the disease course, ideally prior to intubation, through a combination of laboratory abnormalities and respiratory deterioration. we accomplished this by empowering a team of experts in immunology to guide the ordering and interpreting of laboratory tests and the subsequent treatment of covid19-cs patients with corticosteroids and anakinra. this approach resulted in better outcomes compared to the early tocilizumab-treated patients, but our analyses suggest that this could be due to earlier identification and treatment of covid19-cs, rather than superior efficacy of anakinra compared to tocilizumab. in addition, concomitant treatment with corticosteroids may have contributed to the better response observed in the anakinra-treated group, as supported by the preliminary findings of the uk randomized evaluation of covid-19 therapy (recovery) trial (university of oxford, 2020). an exuberant hyper-inflammatory response to covid-19 is increasingly recognized as a major cause of morbidity and mortality in these patients (mehta et al., 2020) . while still not fully understood, covid19-cs appears to start 8-10 days after onset of symptoms and is characterized clinically by high fevers, dyspnea, hypoxemia and bilateral pulmonary infiltrates, and can progress rapidly to ards and multisystem organ failure with or without hypercoagulability and, ultimately, death. in severe forms of cytokine storm due to mas and hlh, the current standard of care includes prompt identification through a combination of laboratory abnormalities and symptoms followed by early treatment with anakinra alone or in combination with corticosteroids (halyabar et al., 2019) . a rapid clinical response is expected, including resolution of fevers, hypotension and improvement in inflammatory markers (lee et al., 2014) ; if not, doses are escalated, often requiring treatment with continuous iv anakinra. in these patients, anakinra is preferred over tocilizumab because it targets il-1, an upstream cytokine in cs. in addition, it can be titrated based on cs severity and easily stopped should serious infection occur. a long half-life, and blunts crp and ferritin levels in the absence of clinical response, which can lead to confusion and delays in escalating treatment (halyabar et al., 2019) . tocilizumab is fda-approved for the treatment of a milder form of cytokine storm (renamed cytokine release syndrome) caused by t-cell inducing cancer therapies (car-t) and is used as an escalation therapy in these patients should corticosteroids fail. while it is unclear why tocilizumab was chosen over anakinra in the early covid-19 outbreak, we speculate that it may be because il-6, unlike il-1, is relatively easy to measure in serum. this led to studies showing an association between high serum il-6 levels and poor covid-19 prognosis (zhou et al., 2020 ) and a subsequent case series reporting on the use of subcutaneous tocilizumab at doses similar to ours in combination with corticosteroids (xu et al., 2020) . it should be noted that il-6 serum levels take 3 or more days to return in the u.s. and thus are not useful in making treatment decisions in rapidly deteriorating patients. the findings from the initial case series (xu et al., 2020) differ from ours in that only 2 of 21 patients required mechanical ventilation, all patients were treated with concomitant corticosteroids and the majority of patients showed rapid improvement (xu et al., 2020) . in contrast, the majority of our tocilizumab-treated patients required invasive ventilation, did not receive corticosteroids and few j o u r n a l p r e -p r o o f showed rapid improvement, suggesting that tocilizumab alone is unlikely to be effective in later stages of covid19-cs. more recently, an italian group reported findings using high dose iv tocilizumab (8mg/kg, 2-3 doses) to treat 100 patients with respiratory failure from covid19-cs in combination with high-dose dexamethasone (20mg/day) in italy (toniati et al., 2020) . this group (toniati et al., 2020) , similar to our study, incorporated laboratory abnormalities based on hlh to identify treatment candidates and identified 57 patients on the wards with worsening respiratory status, with the remaining 43 in the icu on mechanical ventilation. within 10 days following tocilizumab initiation, 77 patients had improved and 20 had died, 10 of which were on mechanical ventilation at treatment initiation, and 3 others had worsened. fewer patients in this cohort (toniati et al., 2020) appear to have neutrophilia at tocilizumab initiation (median=6700, iqr 4900-9700) compared to our cohort (71.2% >8000), yet neutrophilia was a poor prognostic indicator in both studies. this suggests that one explanation for the improved outcomes reported (toniati et al., 2020) compared to ours may be due to earlier identification of covid19-cs. other possible explanations for improved outcomes in mechanically ventilated covid19-cs patients treated with tocilizumab are co-administration of high dose corticosteroids or higher iv doses of tocilizumab used. this later explanation seems less likely as the patients who died or worsened had increasing il-6 levels (toniati et al., 2020) . we co-administered corticosteroids with anakinra despite the who's recommendations against corticosteroids because the logic of treating cytokine storm, an aberration that involves multiple cytokines, by targeting a single cytokine in critically ill patients is problematic. corticosteroids have broad immunological effects that may dampen unique features of covid19-cs including neutrophilia (barnes et al., 2020) and platelet activation. the recognition of some of these unique features of covid19-cs is also why we adapted mas/hlh criteria to include lymphopenia and neutrophilia and no longer screen for low levels of fibrinogen as an early indicator of covid19-cs. neutrophilia appears to be late finding in covid19-cs, and along with aki and hypotension, was more common at treatment initiation in the tocilizumab group. these factors were associated with a lack of response to both tocilizumab and anakinra. longer duration of covid19-cs also appeared to be associated with poor prognosis, but this finding was not statistically significant. early in the covid-19 outbreak, clinicians identified potential tocilizumab candidates based on the development of severe respiratory failure. by assisting hospitalists and icu physicians with monitoring and interpreting covid19-cs labs, we were able to identify patients in cytokine storm often prior to intubation. consequently, treating with anakinra and corticosteroids earlier may have contributed to improved outcomes. the main limitation of this study is the possibility of unmeasured confounding that is present in all observational studies. in addition, we did not compare targeted therapy to treatment with corticosteroids alone or no ant-inflammatory treatments. thus, we cannot exclude the possibility that neither anti-cytokine treatment is superior to corticosteroids alone, particularly in non-intubated patients. the small sample size is another limitation. while the apparent superiority of anakinra and corticosteroids over tocilizumab was not statistically significant at a point estimate of 54%, it is possible that the study was underpowered. the anakinra doses we used were also lower than those reported out of italy (cavalli et al., 2020) . it is possible that higher doses of anakinra may prove to be more effective than lower anakinra doses (cavalli et al., 2020) or than anti-il6 agents, particularly when administered early in covid-cs prior to intubation. another limitation is that only tocilizumab was used early in the outbreak whereas a month later, both tocilizumab and anakinra were used, raising the possibility that secular trends in care may have contributed to the results. while we did our best to capture the other aspects of improved covid-19 care (lab monitoring in non-icu patients, recognition that hyperinflammation often corresponds with increasing o2 requirements and precedes intubation) and accounted for this in the statistical analysis, residual confounding from other improvements in care j o u r n a l p r e -p r o o f would further reduce differences in outcomes across treatment groups. another possibility is that the stay-at-home orders in effect later in the study period may have led to an overall shift to milder disease in admitted patients. however, this does not seem to be the case in our study, as comorbidities associated with poor covid-19 outcomes (zhou et al., 2020) were more common in the anakinratreated group. lastly, the covid19-cs lab criteria used in this study were adapted from the existing mas/hlh criteria based on limited experience. it is likely that the panel could be simplified, tailored to individuals and a risk score developed. this should be addressed in future studies. some studies have relied primarily on crp (xu et al., 2020) or crp and ferritin (cavalli et al., 2020) to identify hyperinflammation and response to anti-inflammatory agents. this may be a reasonable approach for treatment with corticosteroids or anakinra, but other inflammatory markers would need to be monitored following treatment with anti-il6 agents because they can blunt crp and ferritin levels in the absence of a clinical response. the strengths of this study are the importance of the question, the population-based sample, and the team-based approach to recognizing and treating covid19-cs. in many clinical settings, tocilizumab and, to a lesser extent anakinra, are being used to treat covid-19 patients with very little information to guide patient selection, dosing or monitoring of treatment response. our most important finding is that covid19-cs lab abnormalities may be the earliest signal to alert clinicians to initiate cs treatment prior to respiratory failure. not measuring cs labs and delayed treatment, including with corticosteroids, may have contributed to worse outcomes in the tocilizumabtreated patients. randomized controlled trials of targeted anti-cytokine treatments should report duration of elevated covid19-cs inflammatory markers in addition to clinical severity at randomization. because of their wide availability, low cost and pleiotropic anti-inflammatory properties, corticosteroids should be compared with targeted anti-cytokine treatments. studies to identify a parsimonious set of laboratory indicators of covid-19-related hyperinflammation are also urgently needed. j o u r n a l p r e -p r o o f ( .0001 4 (40.0) *comparing extubated to dead patients, chi-square or fisher exact test and wilcoxon rank-sum **among patients intubated at treatment initiation ***excludes 3 patients with missing labs ****excludes 5 patients missing wbc labs (n=3 dead, n=2 still intubated) *****excludes 4 patients missing labs at last follow-up (n=1 extubated, n=2 still intubated, n=1 dead) abbreviations: sd=standard deviation; med=median; iqr=interquartile range; sx=symptom; bmi=body mass index; copd=chronic obstructive pulmonary disease; covid19-cs=coronavirus 2019-related cytokine storm; µl=microliter; y=years; d=days, cs=cytokine storm; scr=serum creatinine j o u r n a l p r e -p r o o f targeting potential drivers of covid-19: neutrophil extracellular traps interleukin-1 blockade with high-dose anakinra in patients with covid-19, acute respiratory distress syndrome, and hyperinflammation: a retrospective cohort study calm in the midst of cytokine storm: a collaborative approach to the diagnosis and treatment of hemophagocytic lymphohistiocytosis and macrophage activation syndrome challenges in the diagnosis of hemophagocytic lymphohistiocytosis: recommendations from the north american consortium for histiocytosis (nacho). pediatr blood cancer sociodemographic characteristics of members of a large, integrated health care system: comparison with us census bureau data current concepts in the diagnosis and management of cytokine release syndrome covid-19: consider cytokine storm syndromes and immunosuppression tocilizumab for the treatment of severe covid-19 pneumonia with hyperinflammatory syndrome and acute respiratory failure: a single center study of 100 patients in recovery: randomised evaluation of covid-19 therapy effective treatment of severe covid-19 patients with tocilizumab clinical course and risk factors for mortality of adult inpatients with covid-19 in wuhan key: cord-318808-1cfwj5uq authors: li, ying; wang, haizhou; wang, fan; du, hui; liu, xueru; chen, peng; wang, yanli; lu, xiaoxia title: comparison of hospitalized patients with pneumonia caused by covid-19 and influenza a in children under 5 years date: 2020-06-12 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.026 sha: doc_id: 318808 cord_uid: 1cfwj5uq abstract background since the outbreak of coronavirus disease 2019 (covid-19) in wuhan, considerable attention has been paid on its epidemiology and clinical characteristics in children patients. however, it is also crucial for clinicians to differentiate covid-19 from other respiratory infectious diseases, such as influenza viruses. methods this was a retrospective study. two group of covid-19 patients (n=57) and influenza a patients (n=59) were enrolled. we analyzed and compared their clinical manifestations, imaging characteristics and treatments. results the proportions of cough (70.2%), fever (54.4%) and gastrointestinal symptoms (14.1%) in covid-19 patients were lower than those of influenza a patients (98.3%, p<0.001; 84.7%, p<0.001; and 35.6%, p=0.007; respectively). in addition, covid-19 patients showed significantly lower levels of leukocytes (7.87 vs. 9.89×109/l, p=0.027), neutrophils (2.43 vs. 5.16×109/l, p<0.001), c-reactive protein (crp; 3.7 vs. 15.1mg/l, p=0.001) and procalcitonin (pct; 0.09 vs. 0.68mm/h, p<0.001), while lymphocyte levels (4.58 vs. 3.56×109/l; p=0.006) were significantly higher compared with influenza a patients. in terms of ct imaging, ground-glass opacification in chest ct was more common in covid-19 patients than in influenza a patients (42.1% vs. 15%, p=0.032). in contrast, consolidation was more common in influenza a patients (25%) than that in covid-19 patients (5.2%, p=0.025). conclusion the clinical manifestations and laboratory tests of covid-19 children are milder than those of influenza a children under 5 years. additionally, imaging results more commonly presented as ground-glass opacities in covid-19 patients. the clinical manifestations of covid-19 children are milder than those of influenza a children under 5 years. the laboratory tests of covid-19 children are milder than those of influenza a children under 5 years. imaging results more commonly presented as ground-glass opacities in covid-19 patients. since december 2019, a novel coronavirus has broken out in wuhan, and spread rapidly worldwide. on february 11, 2020, the world health organization (who) officially named this novel coronavirus pneumonia as coronavirus disease 2019 , whereas the international committee on taxonomy of viruses has named it as severe acute respiratory syndrome coronavirus 2 (sars-cov-2). on 11 march, who declared the covid-19 should be characterized as a pandemic. as the highly contagious of sars-cov-2, the entire population were generally susceptible, including young children. data from china showed young children were vulnerable to sars-cov-2 infection (dong et al., 2020) . in addition, who estimated that more than more than 2 million children under 5 years of age die from pneumonia, accounting for almost one in five under-5 deaths worldwide in 2004 (wardlaw et al., 2006) . pneumonia was the leading infectious cause of death in children younger than 5 years (wardlaw et al., 2006) . therefore, close attention should be paid to children with pneumonia less than 5 years old during the covid-19 pandemic. influenza viruses have precipitated pandemics several times over the past 100 years, specifically in 1918, 1957, 1968 and 2009 . influenza a was a common cause of pneumonia in young children (jain et al., 2015) . recently, kong et al retrospectively investigated the presence of sars-cov-2 among local patients with influenza like illness (ili) from 6 october 2019 to 21 january 2020 and found sars-cov-2 rna was detected in nine ili patient specimens (kong et al., 2020) . in addition, ili data for the 2019-2020 winter was significantly higher in comparison to previous years about children, suggested it was necessary to distinguish the difference between influenza a and covid-19 young children with pneumonia. therefore, the aim of this study was to compare the different clinical page 5 of 15 j o u r n a l p r e -p r o o f 5 presentations between patients with infected with covid-19 pneumonia versus influenza a pneumonia, to provide some recommendations for their differential diagnosis. subjects of the study were consecutive children with either confirmed covid-19 pneumonia (admitted between 28 january and 11 march 2020) or influenza a pneumonia (admitted between 14 december 2019 and 30 february 2020) in wuhan children's hospital. the study was approved by the research ethics board of wuhan children's hospital (no. 2020003) . consent of the patients' legal guardians was obtained. children were included in the study if they had evidence consistent with pneumonia as assessed by means of chest radiography or ct within 72 hours before or after admission. the virus nucleic acid detection kit was confirmed covid-19 patients through detecting the rna of sars-cov-2 in throat swab samples using based on the manufacturer's protocol (shanghai biogerm medical biotechnology co.,ltd). influenza a was detected by direct immunofluorescence assay. the diagnostic criteria for severe pneumonia caused by sars-cov-2 and influenza a conform to guideline (2020, harper et al., 2009 ). a covid-19 or influenza a case report form was designed to document primary data regarding demographic, clinical and laboratory characteristics from electronic medical records. the following information was extracted from each patient: gender, age, medical history, chief complaints, laboratory findings and computed tomography (ct) imaging on admission. categorical data were described as percentages, and continuous data as median with standard deviation (sd). nonparametric comparative test for continuous data and χ 2 test for categorical data were used to compare variables between groups. the statistical analyses were performed using spss statistics version 25.0 software. p<0.05 was considered statistically significant. a total of 57 covid-19 patients and 59 influenza a patients were included (table 1) . no significant differences were found in the median age between covid-19 patients and influenza a patients (18.7 months vs. 21.8 months, p = 0.121). the proportion of male was also not significantly different between the two groups (61.4% vs. 66.1%, p = 0.599). the most common symptoms and signs were cough (84.5%), fever (69.8%) and gastrointestinal symptoms (25%), whereas dyspnea (6.0%) and convulsions (3.4%) were less common. for blood inflammatory indictors, lower levels of c-reactive protein (crp), procalcitonin (pct) were observed in covid-19 patients than influenza a patients ( table 2 ). in terms of ct imaging, ground-glass opacification in chest ct was more common in covid-19 patients than in influenza a patients (42.1% vs. 15%, p = 0.032). in contrast, consolidation was more common in influenza a patients (25%) than that in covid-19 patients (5.2%, p = 0.025) ( fig. 1 and table 3 ). as we found before, cough and fever were the common symptoms in covid-19 (lu et al., 2020) , which is similar with influenza a. our present study revealed that covid-19 manifested as mild, severe pneumonia were less than influenza a patients. some covid-19 patients only presented as fever or cough. meanwhile, influenza a patients were more likely to be fever with higher temperature. gastrointestinal symptoms were supposed to be common in patients with covid-19 (cheung et al., 2020) , however, were less when compared with influenza a. convulsions could be found in both patients, but the reason was different, as only one in covid-19 was secondary to pneumonia and three in influenza a were confirmed as febrile convulsion. lymphopenia and raise in d-dimer were the common laboratory abnormality in covid-19 adult (huang et al., 2020 and were proved as the caution of severity in covid-19 (ruan et al., 2020 , zheng et al., 2020 . in our study, lymphocyte count and d-dimer were lower in influenza a patients than in covid-19, which could further prove that covid-19 is milder than influenza a. similarly, crp (c-reactive protein) and pct (procalcitonin), which was the severity index of pneumonia, were lower in covid-19 than influenza a. in our study, we found that ground-glass opacity was more common in covid-19 patients than in influenza a patients, whereas consolidation was more frequent in influenza a patients, which was consistent with previous studies. the radiological findings of children with covid-19 pneumonia from our team and other study showed that ground-glass opacities were the most common pattern of abnormalities in chest ct (chang et al., 2020) . additionally, studies on influenza a-associated pneumonia showed that consolidation was common on ct (guo et al., 2012) . therefore, these differential pathological changes may contribute to distinguish imaging characteristics during clinical assessments. there were some limitations of our present study. first, this was a retrospective study that included data from a single-center cohort. we hope for prospective cohort and multi-center study. second, influenza a was diagnosis by direct immunofluorescence assay and failed to be typed. in conclusion, covid-19 patients were mild not only in clinical symptoms but also in laboratory examinations which including lymphocyte, crp, pct, d-dimer in the children under 5 years. additionally, imaging results more commonly presented as ground-glass opacity in covid-19 patients. the authors declare that they have no conflict of interest. this study was approved by the research ethics board of wuhan children's hospital (no. whch 2020003). [ gastrointestinal manifestations of sars-cov-2 infection and virus load in fecal samples from the hong kong cohort and systematic review and meta-analysis epidemiology of covid-19 among children in china radiological findings in 210 paediatric patients with viral pneumonia: a retrospective case study seasonal influenza in adults and children--diagnosis, treatment, chemoprophylaxis, and institutional outbreak management: clinical practice guidelines of the infectious diseases society of america. clinical infectious diseases : an official publication of the infectious diseases society of clinical features of patients infected with 2019 novel coronavirus in wuhan community-acquired pneumonia requiring hospitalization among u sars-cov-2 detection in patients with influenza-like illness sars-cov-2 infection in children clinical predictors of mortality due to covid-19 based on an analysis of data of 150 patients from wuhan hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china pneumonia: the leading killer of children mb isoenzyme of creatine kinase; bun, blood urea nitrogen key: cord-343789-6tq0kcfd authors: al-tawfiq, jaffar a.; momattin, hisham; dib, jean; memish, ziad a. title: ribavirin and interferon therapy in patients infected with the middle east respiratory syndrome coronavirus: an observational study date: 2014-01-06 journal: int j infect dis doi: 10.1016/j.ijid.2013.12.003 sha: doc_id: 343789 cord_uid: 6tq0kcfd background: the middle east respiratory syndrome coronavirus (mers-cov) has been reported to have a high case-fatality rate. currently, there is no specific therapy or vaccine with proven effectiveness for mers-cov infections. methods: a combination of ribavirin and interferon therapy was used for the treatment of five mers-cov-positive patients. we reviewed the therapeutic schedule and the outcome of these patients. results: all patients were critically ill with acute respiratory distress syndrome treated with adjunctive corticosteroids and were on mechanical ventilation at the time of initiation of therapy. the median time from admission to therapy with ribavirin and interferon was 19 (range 10–22) days. none of the patients responded to the supportive or therapeutic interventions and all died of their illness. conclusions: while ribavirin and interferon may be effective in some patients, our practical experience suggests that critically ill patients with multiple comorbidities who are diagnosed late in the course of their illness may not benefit from combination antiviral therapy as preclinical data suggest. there is clearly an urgent need for a novel effective antiviral therapy for this emerging global threat. since the discovery of middle east respiratory syndrome coronavirus (mers-cov), the virus has caused 163 cases of disease, with a fatality rate of 43-50%. 1, 2 the disease was initially described in a patient from saudi arabia in june 2012. 3 mers-cov has caused sporadic cases and clusters in families and healthcare settings. [4] [5] [6] [7] the best treatment option for the virus is not known. in view of the high case-fatality rate and the potential global spread of the virus, there is an urgent need to develop effective therapies for this infection. in a recent review, based on therapies used for the related severe acute respiratory syndrome (sars) coronavirus, the possible use of interferon and ribavirin was considered as a therapeutic option. 8 the purpose of this study was to describe the outcome of the use of a combination of interferon-a2b and ribavirin in the management of five patients with mers-cov infections. a 62-year-old woman with diabetes, hypertension, and endstage renal disease (esrd) on hemodialysis was admitted with fever, cough, and respiratory failure of 3-day duration (table 1) . she tested positive for mers-cov by pcr. baseline laboratory data are shown in tables 2 and 3. on admission, the patient was started on oseltamivir 75 mg once daily for 5 days and levofloxacin 500 mg intravenous (iv) every 2 days for 15 days. imipenem was added on day 5 for 3 days. on day 21 after admission, she was started on ribavirin for 5 days with a loading dose of 2000 mg via nasogastric tube, followed by 400 mg per os (po) every 8 h, one dose of interferon-a2b 130 mg subcutaneously, and methylprednisolone 40 mg iv every 8 h for 1 day, then twice daily for 1 day, then daily for 2 days. she had a mild rise in amylase and lipase (from 61 to 126 u/l and from 274 to 348 u/l, respectively). the patient remained critically ill on mechanical ventilation requiring inotropic support. she died 34 days after admission from respiratory and multi-organ failure. a 58-year-old man with diabetes, hypertension, and esrd on hemodialysis was admitted with cough, fever, and hypoxemic respiratory failure of 2-day duration. he tested positive for mers-cov by pcr. baseline laboratory data are shown in tables 2 and 3. on admission, the patient was started on oseltamivir 75 mg once daily for 5 days, levofloxacin 500 mg iv every 2 days for 6 days, and imipenem 250 mg iv twice daily for 7 days. on day 6, he was prescribed methylprednisolone 60 mg iv every 6 h for 6 days, then every 8 h for 1 day, then 40 mg every 12 h for 1 day, followed by a prednisolone tapered dose for another 10 days. on day 13 after admission, he was started on ribavirin for 5 days with a loading dose of 2000 mg po, followed by 400 mg every 8 h and two doses of interferon-a2b 100 mg subcutaneously once per week. two weeks after the initiation of the therapy, platelets dropped from 408 to 43 â 10 9 /l ( table 2 ). the patient remained on the ventilator for more than 30 days. he died 35 days after admission from multiorgan failure. a 63-year-old woman with a history of severe bronchial asthma and obstructive sleep apnea (on continuous positive airway pressure (cpap)), with coronary artery disease, diabetes, hypertension, and chronic kidney disease (estimated glomerular filtration rate 15.7 ml/min), was admitted with fever, cough, and dyspnea of 3-day duration and a diagnosis of pneumonia. she tested positive for mers-cov by pcr. baseline laboratory data are shown in tables 2 and 3. on admission, the patient was also started on oseltamivir 75 mg once daily for 5 days, levofloxacin 750 mg iv every 2 days for 7 days, and imipenem 500 mg iv every 6 h for 8 days. on day 11, she was started on ribavirin for 5 days, with a loading dose of 2000 mg via nasogastric tube followed by 600 mg po every 8 h, one dose of interferon-a2b 144 mg subcutaneously, and prednisone 40 mg po daily, tapered to 10 mg po daily for 10 days. one week after initiation of the antiviral and steroid therapy, serum creatinine, aspartate aminotransferase (ast) tables 2 and 3, and amylase increased (from 0.6 to 2.9 mg/dl, from 6.3 to 20 â 10 9 / l, from 25 to 126 iu/l, and from 35 to 255 u/l, respectively). the patient was diagnosed with pancreatitis and thus further interferon and ribavirin was not given. the patient remained critically ill on mechanical ventilation. she died 45 days after admission from multi-organ failure. an 81-year-old man with a history of atrial fibrillation, diabetes mellitus, and hypertension was admitted with progressive respiratory distress and hypoxemia with fever for 2 days. he tested positive for mers-cov by pcr. baseline laboratory data are shown in tables 2 and 3. on the first day of hospitalization, the patient was started on oseltamivir 75 mg once daily for 6 days, levofloxacin 750 mg every 48 h for 5 days, and imipenem 250 mg iv every 6 h for 6 days. on day 20 after admission, he was started on ribavirin for 9 days, with a loading dose of 2000 mg via nasogastric tube followed by 800 mg via nasogastric tube every 8 h, two doses of interferon-a2b 100 mg subcutaneously once per week on hospital days 20 and 27, and methylprednisolone 40 mg iv every 8 h for 4 days, then 40 mg iv twice daily for 2 days, then 40 mg daily for 2 days (started on hospital day 22). three weeks after the initiation of therapy, his hemoglobin dropped (from 11.7 to 8.7 g/dl) ( table 2) , while bilirubin increased (from 0.7 to 7.4 mg/ dl), suggestive of hemolysis. the patient died 52 days after admission from multi-organ failure. a 24-year-old man with a history of esrd on hemodialysis was admitted with a febrile illness, a cough for 10 days, and respiratory failure requiring mechanical ventilation. he tested positive for mers-cov by pcr. baseline laboratory data are shown in tables 2 and 3. on the first day of hospitalization, the patient was started on oseltamivir 75 mg once daily for 2 days and imipenem 250 mg iv twice daily for 11 days. on day 19 of admission, he was started on ribavirin for 11 days, with a loading dose of 2000 mg via nasogastric tube, followed by 400 mg via nasogastric tube every 8 h, and two doses of interferon-a2b 100 mg subcutaneously once per week on hospital days 19 and 26. on the same day he started ribavirin, he was also started on methylprednisolone 40 mg iv every 8 h for 4 days, then 40 mg iv twice daily for 2 days, and then 40 mg daily for 2 days. two weeks after the initiation of therapy, lipase increased (from 561 to 612 u/l). the patient died 32 days after admission from multi-organ failure. we reviewed the cases of five patients with mers-cov (table 1) . their median age was 62 (range 24-81) years. the patients had chronic kidney disease and four were on maintenance hemodialysis. there were three men and two women. all patients tested negative for influenza. the median number of days from admission to therapy with ribavirin and interferon was 19 (range 10-22) ( table 4 ). all patients received adjunctive corticosteroid therapy for acute respiratory distress syndrome. two patients developed increased lipase after the initiation of therapy, but both of them were given corticosteroids at the same time as antiviral therapy. one patient (case 2) developed thrombocytopenia, with a platelet count that dropped from 408 to 49 â 10 9 /l (tables 2 and 3) and one patient had possible hemolysis (case 3). all patients had severe disease with progressive respiratory failure, developed multi-organ failure, and died a mean 39.6 (standard deviation 8.5) days after admission. none of the patients had bacteremia or fungemia during their hospital stay. figure 1 shows the median, minimum, and maximum values for amylase, lipase, and lactate dehydrogenase (ldh) for all the patients before initiation of therapy and at week1 and 2 after therapy initiation. since the emergence of mers-cov in 2012, the virus has caused a total of 163 cases of disease, with a high case-fatality rate of 43%. 2 there is an urgent need for effective therapeutic agents. to date, no data are available on the use of any agents for the therapy of mers-cov-positive patients. in this report we have described the therapy of five mers-cov patients who received interferon and ribavirin. the patients were treated during the initial phase of the al-hasa outbreak in april and may 2013, a time at which the disease epidemiology and clinical characteristics were not known. hence, there was an inevitable time lapse from admission to the initiation of therapy. all patients were already on mechanical ventilation by the time interferon and ribavirin therapy was instituted and all had a fatal outcome. the patients received the therapy late in the course of the disease, at a median of 19 (range 10-22) days after admission. late therapy may have contributed to the poor outcome, in addition to the severity of the disease and the multiple comorbidities of the patients. the timing of initiation of antiviral therapy is critical in the treatment of most viral infections. in the treatment of sars-cov, no effect of oseltamivir or ribavirin was observed when these agents were started 6-14 days after symptom onset. [11] [12] [13] early therapy with ribavirin, within 48 h of hospitalization or after the diagnosis of sars, has been shown to be associated with better outcomes, although the numbers of patients enrolled in these studies has been small. 7, [14] [15] [16] [17] in the treatment of influenza, oseltamivir therapy early in the disease resulted in reduced mortality when this was started not later than 8 days after the onset of symptoms. 18 early in vitro studies showed that ribavirin and interferon have anti-mers-cov activity. 19 the in vitro activity of interferon was augmented by the concomitant use of ribavirin. 20 in a rhesus macaque model of mers-cov infection, the combination of interferon-a2b and ribavirin therapy was effective in limiting the disease and resulted in very mild radiographic evidence of pneumonia. 21 the treatment was given within 8 h after inoculation of the rhesus macaques. treated animals had lower levels of systemic and local proinflammatory markers and fewer viral genome copies. 21 although these preclinical data are promising, our report illustrates some of the real world issues of dealing with a novel emerging viral infection. our patients were not diagnosed until a week into their illnesses, by which time all five were on mechanical ventilation. they had multiple comorbidities, which most likely adversely affected their clinical outcomes. in addition, we had no serial virologic determination of mers-cov levels in airway secretions to shed light on the possibility of virological clearance, virological failure, or clinical failure of therapy. in our small series, adverse effects from combination ribavirin and interferon therapy were observed in three cases. these side effects have been noted before. 22 two patients had pancreatic enzyme elevation and one had significant hemolysis. these findings were complicated by the presence of abnormal laboratory findings even before the initiation of combination therapy, so it is difficult to determine which side effects were due to disease progression and which were due to the therapeutic drugs. there is an urgent need for large-scale clinical trials to determine the safest and most effective regime for the treatment of this novel highly fatal emerging infection. while ribavirin and interferon may show promise, their use needs to be prompt and adverse effects monitored closely. this therapeutic approach should be tested in careful clinical studies. taking stock of the first 133 mers coronavirus cases globally-is the epidemic changing? middle east respiratory syndrome coronavirus (mers-cov)-update isolation of a novel coronavirus from a man with pneumonia in saudi arabia a family cluster of middle east respiratory syndrome coronavirus infections related to a likely unrecognized asymptomatic or mild case epidemiological, demographic, and clinical characteristics of 47 cases of middle east respiratory syndrome coronavirus disease from saudi arabia: a descriptive study ksa mers-cov investigation team. hospital outbreak of middle east respiratory syndrome coronavirus family cluster of middle east respiratory syndrome coronavirus infections therapeutic options for middle east respiratory syndrome coronavirus (mers-cov)-possible lessons from a systematic review of sars-cov therapy detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction assays for laboratory confirmation of novel human coronavirus (hcov-emc) infections severe acute respiratory syndrome (sars) in singapore: clinical features of index patient and initial contacts severe acute respiratory syndrome: report of treatment and outcome after a major outbreak investigational use of ribavirin in the treatment of severe acute respiratory syndrome identification of severe acute respiratory syndrome in canada a cluster of cases of severe acute respiratory syndrome in hong kong clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study description and clinical treatment of an early outbreak of severe acute respiratory syndrome (sars) in guangzhou, pr china effectiveness of antiviral treatment in human influenza a(h5n1) infections: analysis of a global patient registry broad-spectrum antivirals for the emerging middle east respiratory syndrome coronavirus inhibition of novel b coronavirus replication by a combination of interferon-a2b and ribavirin treatment with interferon-a2b and ribavirin improves outcome in mers-covinfected rhesus macaques product information: rebetol (r) oral capsules solution, ribavirin oral capsules solution the authors (jat, hm, and jd) wish to acknowledge the use of the saudi aramco medical services organization (samso) facilities for the data and study, which resulted in this paper. opinions expressed in this article are those of the authors and not necessarily of samso. the authors thank dr paul anantharajah tambyah of the national university of singapore department of medicine for his critical review of the manuscript.financial support: all authors have no funding. conflict of interest: all authors have no conflict of interest to declare. key: cord-283891-m36un1y2 authors: hu, bisong; qiu, jingyu; chen, haiying; tao, vincent; wang, jinfeng; lin, hui title: first, second and potential third generation spreads of the covid-19 epidemic in mainland china: an early exploratory study incorporating location-based service data of mobile devices date: 2020-05-17 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.048 sha: doc_id: 283891 cord_uid: m36un1y2 abstract objectives the outbreak of atypical pneumonia caused by the novel coronavirus (covid-19) has currently become a global concern. the generations of the epidemic spread are not well known, yet these are critical parameters to facilitate an understanding of the epidemic. a seafood wholesale market and wuhan city, china, were recognized as the primary and secondary epidemic sources. human movements nationwide from the two epidemic sources revealed the characteristics of the first-generation and second-generation spreads of the covid-19 epidemic, as well as the potential third-generation spread. methods we used spatiotemporal data of covid-19 cases in mainland china and two categories of location-based service (lbs) data of mobile devices from the primary and secondary epidemic sources to calculate pearson correlation coefficient,r, and spatial stratified heterogeneity, q, statistics. results two categories of device trajectories had generally significant correlations and determinant powers of the epidemic spread. bothr and q statistics decreased with distance from the epidemic sources and their associations changed with time. at the beginning of the epidemic, the mixed first-generation and second-generation spreads appeared in most cities with confirmed cases. they strongly interacted to enhance the epidemic in hubei province and the trend was also significant in the provinces adjacent to hubei. the third-generation spread started in wuhan from january 17 to 20, 2020, and in hubei from january 23 to 24. no obvious third-generation spread was detected outside hubei. conclusions the findings provide important foundations to quantify the effect of human movement on epidemic spread and inform ongoing control strategies. the spatiotemporal association between the epidemic spread and human movements from the primary and secondary epidemic sources indicates a transfer from second to third generations of the infection. urgent control measures include preventing the potential third-generation spread in mainland china, eliminating it in hubei, and reducing the interaction influence of first-generation and second-generation spreads. an outbreak of atypical pneumonia caused by the 2019 novel coronavirus (covid-19) was recognized from middle january, 2020, in wuhan city, china. the novel coronavirus that infects human was first reported in wuhan, hubei province, china, on december 31, 2019 (zhu et al. 2020) . early confirmed cases were mainly linked to a seafood wholesale market in wuhan (li et al. 2020a; zhu et al. 2020) . epidemiological studies indicate that the covid-19 epidemic has a basic reproductive number between 2 and 3 (li et al. 2020a; wu et al. 2020) , which is lower than the 2003 severe acute respiratory syndrome (sars) (lipsitch 2003; riley et al. 2003) . wuhan is a main transportation hub in central china, several million travelers ventured outward from the epidemic outbreak source in the first half of january, 2020, due to annual chinese (lunar) new year holiday migrations. the large-scale outbreak started on january 19 (the first confirmed case reported outside hubei province). although strict transportation screening measures were activated by many cities in the next 3-4 days, the epidemic rapidly spread nationwide in a week. moreover, covid-19 infections have been identified in other countries and the current epidemic has become a global concern (cohen and normile 2020; holshue et al. 2020; rothe et al. 2020; . the world health organization (who) declared the covid-19 outbreak as a public health emergency of international concern (pheic) on january 30 (who 2020b) . there is evidence that the epidemic outbreak in china and elsewhere spread along the paths of travel from wuhan (li et al. 2020b) , and local outbreaks could appear in other major cities of china with time lags (wu et al. 2020) . massive human movements via railways and domestic/international airlines from wuhan, and the timing of chinese new year, has enabled the virus to spread nationwide and worldwide (peeri et al. 2020) . control measures (e.g., travel quarantine and restrictions) in wuhan were effective to delay the overall epidemic progression in mainland china and reduce the international case importations (chinazzi et al. 2020) . the huanan seafood wholesale market and wuhan were recognized as the primary and secondary epidemic centers, respectively, and therefore, the movements of populations from the two sources influenced the generations of the covid-19 epidemic in mainland china, especially during the very early epidemic stage before the transportation measures activated by wuhan and other cities. the first-generation (primary) spread of the epidemic was in part reflected by the human movement from the primary source (i.e., the seafood market), and the secondgeneration (secondary) spread was reflected by that from the secondary center (i.e., wuhan city). they varied and interacted by region and time during the early epidemic progression, and had the potential clues to identify the third-generation spreads in various regions, which are mainly caused by the local cases instead of the imported ones. here, using location-based service (lbs) data of mobile devices, we analyzed the spatiotemporal association of the confirmed covid-19 cases and human movements from the sources of the epidemic outbreak, and revealed the first, second and potential third generation spreads of the covid-19 epidemic in mainland china. we collected spatiotemporal data of covid-19 cases in mainland china from the daily bulletins of the national health commission of the people's republic of china (nhc) and various provincial/municipal health commissions. some publicly available news and media were utilized as supplemental data. the final epidemic dataset was comparatively verified through the public platform of the 2019-ncov-infected pneumonia epidemic from the chinese center for disease control and prevention (china cdc 2020a) . the dataset of the covid-19 cases includes the following fields: date (starting from january 10, 2020), province code/name, city code/name, and numbers of daily new suspected/confirmed cases. from the above dataset, we can generate the cumulative number of daily confirmed cases at a specific city s and until a given end date t, which is denoted by ys,t. the human movement of populations from two epidemic sources (the huanan seafood wholesale market and wuhan), were considered to be associated with the spatiotemporal epidemic spread. the datasets of lbs requests from mobile devices were provide by wayz inc., shanghai, china. the device trace datasets cover over 80% mobile devices supported by the three telecommunication operators in china. the lbs-requesting statistics are implemented every two hours with highresolution location information. the raw data indicate the individual trajectories of numerous mobile devices with high-resolution spatiotemporal information, and can be easily aggregated in a specific spatial scale and within a given time step. for a subpopulation from the epidemic center, we can aggregate the device trace data from the start date to a given end date t, and the corresponding cumulative number at a specific city s is denoted by xs,t. multiple lbs requests within a time step are only counted once by a same device. private individual information was deleted from the raw data of the mobile devices, and in this study, the device trace data was aggregated to the administrative cities and the epidemic date, i.e., the mobile device traces were associated with the j o u r n a l p r e -p r o o f epidemic dataset according to date and location. these aggregated statistics of mobile device traces are expected to be representative of the human migrations from the epidemic sources. two epidemic sources were considered, including the seafood wholesale market and wuhan city. the devices which activated their lbs requests in the market in november 2019 indicated the potential first-generation cases of the covid-19 epidemic. and the potential second-generation cases were those which were activated in wuhan in december 2019 and then traveled to other regions in january 2020. , ( ) and , ( ) are used to denote the spatiotemporal trajectories of the above two subpopulations of mobile devices, respectively. all the processing and aggregation of mobile device trace data were implemented by the provider. the final datasets include the daily counts of two categories of trajectories in all the administrative cities in mainland china. the cumulatively summed device traces had a spatially distributed consistency with the population distribution in mainland china ( figure 1 ). two categories of trajectories mainly spread to the provinces adjacent to hubei and several developed areas a longer distance from hubei, such as guangdong province, zhejiang province and beijing. we considered the spread of the epidemic from the source in various space and time domains, and the corresponding associations with human movements were analyzed in several temporal divisions and spatial scales. seven areas were delineated, including i) wuhan city, ii) hubei province excluding wuhan, iii) hubei province, iv) hubei's adjacent provinces (anhui, chongqing city, henan, hunan, jiangxi and shaanxi), v) mainland china excluding hubei, vi) mainland china excluding wuhan, and vii) mainland china. date periods were generated using three key date stamps, including january 10, 2020 (when the first 41 confirmed cases were reported in wuhan), january 19 (when the large-scale outbreak started) and january 26 (the end of the first week of the largescale outbreak). based on the above datasets of covid-19 cases in mainland china and two categories of location-based service data of mobile devices from the epidemic sources, we calculated their pearson correlation coefficient, r, and spatial stratified heterogeneity (ssh), q, statistics. pearson correlation is usually used to evaluate the linear association between two variables and calculated as follows: (1) where rxy denotes the correlation coefficient of covid-19 spatiotemporal spread and human migrations from the epidemic source, within the period from the start date to a given end date t. ys,t is the cumulative number of daily confirmed cases at city s and xs,t is the cumulative number of device trajectories from the epidemic source, with the mean values of ̄ and , respectively. n is the number of the administrative cities in mainland china. in this study, we calculated two pearson correlations with the spatiotemporal data of two categories of trajectories, , ( ) and , ( ) , to explore the associations between the epidemic spread and the human migrations from the seafood market and wuhan, respectively. the geodetector q statistic is generally applied to quantitatively evaluate the ssh of an explained j o u r n a l p r e -p r o o f variable (wang et al. 2010 (wang et al. , 2016 , and assess the determinant power of explanatory variables and their interaction, without linear assumptions (yin et al. 2019) . the fundamental formula of the q statistic is given by: where q is the determinant power of the factor to the objective. n is the number of objective variable observations and σ 2 indicates the variance of all the observations. the objective is stratified into l stratums, denoted by h =1, 2, …, l, which is determined by the determinant factor. nh is the number of observations and ℎ 2 is the corresponding variance within stratum h. the value of q ranges from 0 to 1. we calculate q statistic to assess the determinant power of human migrations from the epidemic source to covid-19 spatiotemporal spread. similarly, the spatiotemporal data of two categories of trajectories can be applied to calculate two q statistics for the two epidemic sources. within the period from the start date to a given end date t, we implemented the stratification by the equalinterval division after ordering the trajectory data, xs,t, and divided all the observations into 5 strata to calculate the q statistic of the cumulative trajectories, xs,t, to the cumulative cases, ys,t. this is a common stratification way to deal with the numerical independent variables (yin et al. 2019) , which can reduce the subjective influence of various stratifications to q statistics. moreover, for two or more determinant factors, an interaction q statistic can be calculated to measure their interaction influences (e.g., are they independent, or do they weaken/enhance each other?) (wang et al. 2010) . in this study, two categories of trajectories, , ( ) and , ( ) , were used to implement the stratifications and the corresponding q statistics were calculated, respectively, which are denoted by q (m) and q (w) . while the stratification was generated by the intersection between the above two individual stratifications, an interaction q statistic, q (m∩w) , can be calculated, where the symbol "∩" denotes the intersection between two strata layers. various interaction types can be defined according to the comparison between q (m) , q (w) and q (m∩w) (wang et al. 2010) . for instance, "q (m∩w) > q (m) and q (w) " indicates a bi-enhancement interaction between two categories of trajectories in facilitating the spread of the epidemic (see wang et al. 2010 for more details about the interaction q statistic). analyses in this study were performed with the use of the r software package (r foundation for statistical computing) and thematic mapping was implemented in the arcgis platform (esri). similar to the spatial distributions of the mobile device traces (figure 1 ), the pearson correlations r and q statistics between the cumulatively summed cases and two categories of trajectories up to january 26, 2020 had a spatially distributed consistency with the population distribution among the administrative cities in mainland china ( figure 2 ). two categories of trajectories had generally significant correlations and determinant powers of the epidemic spread, and both r and q decreased in distance from the epidemic sources. the first-generation and second-generation transmissions of the infection simultaneously appeared in many cities at the early stage of the outbreak. specifically, devices activated in the market displayed higher values of r and q in several small and medium cities than devices activated in wuhan city (figures 2a and 2c) . it is clear that many cities executed a quick response and activated transportation control measures, which helped control the first-generation epidemic spreads. the r and q statistics of the devices activated in wuhan, however, indicate that the second-generation spread still influenced many cities in the first week of the outbreak ( figures 2b, 2d and table 1 ). the market trajectories received a much higher pearson correlation value to confirmed cases in wuhan (r=0.6160, p<0.001) than hubei province excluding wuhan (r=0.3741, p<0.001) and mainland china excluding hubei (r=0.3319, p<0.001) . the correlations of wuhan trajectories were 0.7438, 0.5874 and 0.5183 in the above three areas, respectively. the temporal correlation curves of both market and wuhan trajectories have obvious decreasing trends from january 17 to 20, 2020 in wuhan ( figure 3a) , which indicates the potential start date of the third-generation epidemic spread. one week after this, market trajectories had higher pearson correlation values than wuhan trajectories, and the first-generation spread still had a serious influence in wuhan ( figure 3a) . similarly, in hubei province excluding wuhan, the potential start date of the third-generation spread was from january 23 to 24 ( figure 3b) . moreover, the second-generation spread played a dominant role in the areas outside wuhan, especially in hubei province excluding wuhan and the provinces adjacent to hubei, since wuhan trajectories had much higher values of correlations ( figures 3b and 3c ). we found no obvious turning dates in the areas outside hubei ( figures 3c and 3d) , and the potential third-generation spread remains to be determined. the curves have remained stationary since january 22 in mainland china excluding hubei ( figure 3d ). the transportation control measures activated by many cities since january 21 appeared to have been successful in partially controlling the first-generation and second-generation epidemic spreads outside hubei province. we focused on the first week of the large-scale outbreak and calculated the q statistics of the two device-activation categories in introducing cumulative confirmed cases in various areas (table 1) . the determinant powers of both categories were extremely high and consistent in wuhan (q=0.8909, p<0.05). their temporal curves had the obvious decreasing trends from january 17 to 20 ( figure 4a ), which validated the start date of the third-generation spread in wuhan. similar validation was observed in hubei province excluding wuhan ( figure 4b ). two categories of trajectories can explain nearly 100% ssh of the epidemic spread in wuhan before the large-scale outbreak and the ssh increased constantly since the third-generation spread stage ( figure 4a ). the market and wuhan trajectories had close determinant powers in introducing the epidemic spread in hubei province (q=0.4153, q=0.4261, respectively, and p<0.001). the q statistics reported that these two categories explained 41.53% and 42.61% ssh of the confirmed cases in hubei. the determinant powers of the epidemic spread in hubei province excluding wuhan were 0.2084 (p<0.01) and 0.2513 (p<0.001), respectively. the q statistic values decreased in distance outside wuhan or hubei and showed that the determinant powers in mainland china excluding hubei were 0.1610 (p<0.001) and 0.1723 (p<0.001), respectively. in the first week of the outbreak, wuhan trajectories received higher values of q statistics than market trajectories in hubei province excluding wuhan and in provinces bordering hubei ( figures 4b and 4c) . the second-generation spread contributed more influence in the areas surrounding the epidemic source. however, both two categories had close q statistic values in mainland china excluding hubei ( figure 4d ). the epidemic outside hubei province appeared as a balanced pattern of mixed first-generation and second-generation spreads. furthermore, the q statistics increased constantly outside hubei province, indicating the increasing ssh of the epidemic spread ( figures 4c and 4d ). more attention should be given to control of the trend of second-generation spread and to eliminate potential third-generation spread. taking into consideration of the interaction influences of two categories of trajectories, the interaction q statistics were calculated in various areas (table 1) . all the interaction types were bienhancement which indicates that two determinant factors (i.e., two categories of trajectories originated from two epidemic sources) enhance each other (the interaction q statistic is higher than each single q statistic but lower than the sum of two single q statistics). the determinant powers and interactions of two categories of trajectories in introducing the epidemic spread decreased in distance from the source to the rest of the nation. the interaction q statistic was 0.1925 (compared to the single q statistics of 0.1610 and 0.1723) in mainland china excluding hubei. the interaction q statistic was 0.0786 (compared to the single q statistics of 0.0657 and 0.0642) in mainland china. although the interaction strength was weak, the combination of both trajectory categories still carried more information about the spread of the epidemic throughout the country. the interaction q statistic of two categories of trajectories in hubei province excluding wuhan was 0.4063, which was close to the sum of two single q statistics (0.2084 and 0.2513) and much higher than each one individually. this interaction indicates strong bi-enhancement in facilitating the spread of the epidemic. two categories of trajectories could significantly enhance each other to explain the ssh of the epidemic spread from wuhan to other areas in hubei province. the majority of the earliest cases of the covid-19 atypical pneumonia were linked to the seafood wholesale market in wuhan, which is the most severely-affected city of the covid-19 outbreak. the movements of populations from these two epidemic sources provided potential first-generation and second-generation spreads nationwide and worldwide. here, based on lbs-requesting mobile device traces and spatiotemporal confirmed covid-19 case data, we applied pearson correlation and geodetector q statistics to analyze the spatiotemporal association between the confirmed cases' dynamic and human movements. our findings provide important foundations to quantify the effect of human movement on the epidemic spread, to judge the epidemic generations, and to inform ongoing and future control strategies. we concentrated on two datasets of lbs-requesting mobile devices associated with two sources linked to the first-generation and second-generation spreads provincewide and nationwide. their traces were aggregated by date in administrative cities and linked to the spatiotemporal confirmed cases. it is notable that the covid-19 outbreak had a strong consistency with human migrations from the epidemic sources. the confirmed cases had a clear linear correlation with two categories of trajectories from the sources to the rest of the nation. moreover, both trajectory categories could generally indicate the epidemic spread in hubei province and explain to a certain extent the ssh of the spread from wuhan to the rest of hubei province and throughout the rest of china. our analyses provide a new perspective to explore the spread of the epidemics linked to human movement. during the first week of the large-scale outbreak, the epidemic spread showed a spatially distributed consistency with the population distribution in mainland china. the majority of cities with confirmed cases had a mixed pattern of first-generation and second-generation spreads at the very beginning of the outbreak. many cities activated quick response within 3-4 days and achieved efficient results in inhibiting the first-generation spread outside hubei province. however, it still had a significant impact in hubei province, especially playing the dominant role inside wuhan city. furthermore, among the other cities in hubei province, the first-generation and second-generation spreads enhanced each other with a much higher interaction q statistic. this might be another signal to identify the potential start date of the third-generation spread in a specific area. due to the quick response and strict control measures in many cities, the interaction enhancement of the firstgeneration and second-generation spreads had a weak strength outside hubei province. there is no evidence that any third-generation spread appeared outside hubei in mainland china in the first week of the outbreak. nevertheless, hubei's adjacent provinces require more effective control measures, since the first-generation and second-generation spreads had an increasing trend. our analyses determined an appropriate approach to explore the spatiotemporal association between the epidemic transmission and human movement. two categories of lbs-requesting mobile devices were used in this study to identify the potential close contacts to the primary and secondary epidemic sources. the datasets covered most devices with lbs requests in the given region and time period. however, the linkage between mobile devices and populations could be subject to information loss (e.g., users may replace their mobile devices with new ones). it is also extremely difficult to cover 100% potential close contacts in our datasets. the close contacts of these two populations while traveling before/after the outbreak were not collected, and therefore we cannot estimate the potential third-generation cases and their movements. this limitation involves future work with more universal-source data and high-performance computing capabilities. the covid-19 epidemic data were collected through publicly available sources, and we processed the data of confirmed cases and device traces in the spatial scale of cities. small-scale analyses could be more helpful to construct epidemic control programs in counties or communities within a city. the spatiotemporal association between the spread of the epidemic and human movements indicates a transfer from second to third generations of the infection. this approach has made it possible to assess the start date of the third-generation spreads of covid-19 epidemic and the interactions between first-generation and second-generation spreads across various regions all over the country. the proposed technique incorporating location-based service data of mobile devices can help identify the spatiotemporal generations at the early stage of the covid-19 epidemic. it can be easily implemented and extended to the early exploratory study of other epidemics similar to covid-19. the results indicate the spatiotemporal characteristics of the epidemic spread associated to human movements from epidemic sources and the potential spatiotemporal risks at the early stage of the outbreak. control measures varying by location and time could be executed in different levels for various regions. for instance, cities with obvious third-generation spread require the strictest controls on both the exportations and the inside quarantine, cities should pay more attention to the importations and the inside quarantine if the first-generation and second-generation spreads have the strong interactive enhancements, and other cities require to focus on the control of the importations. in conclusion, we found that the third-generation spread of the covid-19 outbreak probably started during january 17 to 20, 2020 in wuhan, the potential start date of the third-generation spread in hubei province excluding wuhan was from january 23 to 24, and the mixed first-generation and second-generation spreads strongly interacted to enhance the epidemic. the trend of the interactions between the first-generation and second-generation spreads was significant in the provinces adjacent to hubei. the associations between the epidemic spread decreased with distance and had different temporal pattens from the epidemic sources, implying the potential epidemic generation-togeneration evolution on regional spatial scales. at the very beginning of the outbreak, the mixed first-generation and second-generation spreads appeared in most cities with confirmed cases. no obvious third-generation spread was detected outside hubei province. the strict transportation measures implemented in many cities appeared to have been effective in preventing any thirdgeneration spread nationwide. the urgent control measures in hubei province include weakening the third-generation spread and the interaction influence of the first-generation and secondgeneration spreads. even with strict control strategies, effective measures to reduce transmission in the community are still required (li et al. 2020a) . a large increase in migration due to people returning from travel after the new year holiday also introduces challenges to epidemic control . we recommend the urgent control measures of preventing potential thirdgeneration spread in mainland china, eliminating it in hubei, and reducing the interaction influence of first-generation and second-generation spreads. no individual data was collected and the ethical approval or individual consent was not applicable. the lbs-requesting mobile device data were provided by wayz inc., shanghai, china and are not available for distribution due to the constraint in the consent. the dataset of the covid-19 cases is available from multiple public sources. this work was supported by the national natural science foundation of china (41531179) , the national science and technology major project of china (2016yfc1302504) and the science and technology major project of jiangxi province, china (2020ybbgw0007). the funders had no role in study design and conduct; data collection, management, analysis and interpretation; manuscript preparation, writing and review; decision to submit the manuscript for publication. conceptualization we declare no competing interests. public platform of the 2019-ncov-infected pneumonia epidemic the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak new sars-like virus in china triggers alarm first case of 2019 novel coronavirus in the united states early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia potential of large 'first generation' human-to-human transmission of 2019-ncov transmission dynamics and control of severe acute respiratory syndrome the sars, mers and novel coronavirus (covid-19) epidemics, the newest and biggest global health threats: what lessons have we learned? transmission dynamics of the etiological agent of sars in hong kong: impact of public health interventions transmission of 2019-ncov infection from an asymptomatic contact in germany a novel coronavirus outbreak of global health concern. the lancet what to do next to control the 2019-ncov epidemic? the lancet geographical detectors-based health risk assessment and its application in the neural tube defects study of the heshun region, china a measure of spatial stratified heterogeneity emergency committee regarding the outbreak of novel coronavirus (2019-ncov) nowcasting and forecasting the potential domestic and international spread of the 2019-ncov outbreak originating in wuhan, china: a modelling study. the lancet mapping the increased minimum mortality temperatures in the context of global climate change a novel coronavirus from patients with pneumonia in china we thank dr. adam thomas devlin at the school of geography and environment, jiangxi normal university for the assistance in the proofreading work for the manuscript. j o u r n a l p r e -p r o o f key: cord-340410-s9haq8y1 authors: fukumoto, tatsuya; iwasaki, sumio; fujisawa, shinichi; hayasaka, kasumi; sato, kaori; oguri, satoshi; taki, keisuke; nakakubo, sho; kamada, keisuke; yamashita, yu; konno, satoshi; nishida, mutsumi; sugita, junichi; teshima, takanori title: efficacy of a novel sars-cov-2 detection kit without rna extraction and purification date: 2020-06-26 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.074 sha: doc_id: 340410 cord_uid: s9haq8y1 abstract rapid detection of sars-cov-2 is critical for the diagnosis of coronavirus disease 2019 (covid-19) and preventing the spread of the virus. a novel “2019 novel coronavirus detection kit (ncov-dk)” halves detection time by eliminating the steps of rna extraction and purification. we evaluated concordance between the ncov-dk and direct pcr. the virus was detected in 53/71 (74.6%) and 55/71 (77.5%) by the direct pcr and ncov-dk, respectively, with overall concordance rate of 94.4%: 95.2% in nasopharyngeal swab, 95.5% in saliva, and 85.7% in sputum. the ncov-dk effectively detects sars-cov-2 in all types of the samples including saliva, while reducing time required for detection, labor, and risk of human error. this is a pdf file of an article that has undergone enhancements after acceptance, such as the addition of a cover page and metadata, and formatting for readability, but it is not yet the definitive version of record. this version will undergo additional copyediting, typesetting and review before it is published in its final form, but we are providing this version to give early visibility of the article. please note that, during the production process, errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. takanori teshima, m.d., ph.d. department of hematology, hokkaido university faculty of medicine n15 w7, sapporo, e-mail: teshima@med.hokudai.ac.jp rapid and accurate detection of sars-cov-2 is critical for the prevention of outbreaks of coronavirus disease 2019 in communities and hospitals. the diagnosis of covid-19 is made by real-time quantitative pcr (rt-qpcr) testing of specimens collected by nasopharyngeal swabs (wang et al., 2020 , zou et al., 2020 . however, swab sample collection poses a risk of viral transmission to healthcare workers. self-collecting saliva reduces a risk of health care workers. we and others have shown efficacy of saliva j o u r n a l p r e -p r o o f 4 as a diagnostic tool (azzi et al., 2020 , iwasaki et al., 2020 , williams et al., 2020 , wyllie et al., 2020 . the 2019 novel coronavirus detection kit (ncov-dk, shimadzu corporation, kyoto, japan) eliminates the steps of rna extraction and purification by using the ampdirect tm technology (nishimura et al., 2010) , thus significantly reducing the time required for sample preparation and pcr detection from more than 2 hours to about 1 hour. in addition, the risk of human error during rna extraction can be reduced. however, it remained to be elucidated whether saliva samples could be applied to the ncov-dk, since saliva has high rnase (pandit et al., 2013) . we herein compared efficacy of the ncov-dk with the direct pcr method requiring rna extraction and purification. samples were collected from 9 patients with covid-19, as previously described (iwasaki et al., 2020) . a total of 71 frozen stock samples were available from these patients, with a median of 8 samples (range, 2-15) per patient. this study was approved by the institutional ethics board and informed consent was obtained from all patients. agreement between the two methods was assessed using cohen's kappa. pearson's correlation coefficient test was performed to identify the relation of the ct values between the methods. statistical analyses were performed with ezr (jichi medical university, saitama, japan). p-value of 0.05 was the cutoff for statistical significance. we first examined whether the freeze-thaw step could affect the availability of viral rna for detection. the ncov-dk pcr was performed in 3 fresh samples and the corresponding freeze-thaw specimens. ct values did not change significantly after the freeze-thaw steps (supplementary figure 1) . we then evaluated the viral detection rates in 71 specimens. the virus was detected in 53 (74.6%) fresh samples by the direct pcr and in 55 (77.5%) of the corresponding frozen j o u r n a l p r e -p r o o f samples by the ncov-dk (table 1 ). the overall concordance rate of the virus detection between the two methods was 94.4% (95% ci, ). interrater reliability of the two methods was strong (=0.85), as judged by cohen's kappa analysis. concordance rates were 95.2% (95% ci, 83.8-99.4), 95.5% (95% ci, 77.2-99.9), 85.7% (95% ci, 42.1-99.6) in nasopharyngeal swab, saliva, and sputum samples, respectively. figure 2 shows a scatter plot presenting a comparison of ct values in each sample between the two methods. there was a strong correlation between the two methods (r = 0.837, 95%ci = 0.736-0.902, p < 0.01). significant correlations were also demonstrated in each sample type (swab, r = 0.82, 95%ci = 0.673-0.905, p < 0.01; saliva, r = 0.818, 95%ci = 0.507-0.94, p < 0.01; sputum, r = 0.945, 95%ci = 0.574-0.994, p < 0.01). we demonstrate that a novel sars-cov-2 detection kit ncov-kd is as effective as the direct pcr in detecting sars-cov-2 in all types of the samples. particularly, it should be noted saliva is a reliable tool to detect the virus by the ncov-kd even without process of rna extraction and purification. there are some discordant results between the two methods. the virus was detected only by the direct pcr in one sample, while the virus was detected only by the ncov-dk in 3 samples. it is unclear whether these are false-positive or j o u r n a l p r e -p r o o f saliva is a detect sars-cov-2 comparison of sars-cov-2 detection in nasopharyngeal swab and saliva detection of noroviruses in fecal specimens by direct rt-pcr without rna purification high-yield rna-extraction method for saliva consistent detection of 2019 novel coronavirus in saliva detection of sars-cov-2 in different types of clinical specimens saliva as a non-invasive specimen for detection of sars-cov-2 saliva is more sensitive for sars-cov-2 detectionin covid-19 patients than nasopharyngeal swabs this work was in part supported by grants from japan medical association policy research organization (jmari). the authors declare that they have no competing interests. key: cord-332348-yi85sfks authors: liang, yujie; xu, jiabin; chu, mei; mai, jianbo; lai, niangmei; tang, wen; yang, tuanjie; zhang, sien; guan, chenyu; zhong, fan; yang, liuping; liao, guiqing title: neurosensory dysfunction: a diagnostic marker of early covid-19 date: 2020-06-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.086 sha: doc_id: 332348 cord_uid: yi85sfks abstract objectives to detailly described the neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, in patients with covid-19. methods clinical characteristics and oropharyngeal swabs were obtained from 86 patients with covid-19 hospitalized in guangzhou eighth people’s hospital. chronological analysis method was used to detailly clarify the neurosensory dysfunction. the cycle threshold (ct) values were used to approximately indicate viral load. results forth-four (51.2%) patients had neurosensory dysfunction: hyposmia (34, 39.5%), hypogeusia (33, 38.4%), and tinnitus (3, 3.5%). neurosensory dysfunction was significantly more common in patients under 40 years old (p = 0.001) or women (p = 0.006). hyposmia and hypogeusia coexisted in 23 (26.7%) patients. the interval between onset of hyposmia and hypogeusia was 0.7 ± 1.46 days. the interval from onset of hyposmia and hypogeusia to typical symptoms was 0.22 ± 4.57 and 0.75 ± 6.77 days; the interval from onset of hyposmia and hypogeusia to admission was 6.06 ± 6.68 and 5.76 ± 7.68 days; and the duration of hyposmia and hypogeusia was 9.09 ± 5.74 and 7.12 ± 4.66 days, respectively. the viral load was high since symptoms onset, peaked within the first week, and then gradually declined. conclusions the neurosensory dysfunction tends to occur in the early stage of covid-19, and it could be used as a marker for early diagnosis of covid-19. a global pandemic named coronavirus disease 2019 , caused by sars-cov-2 infection, has been wreaking havoc with the health of much of human civilization. by april 30, 2020, a total of more than 3 million patients with had been confirmed worldwide, including over 217 thousand deaths [1] . early diagnosis is key to the management of the covid-19 pandemic. recently, some researchers have reported that patients with covid-19 would suffer from neurosensory dysfunction, including loss of smell (hyposmia) and taste (hypogeusia), with a prevalence of 5.1%-98% [2] [3] [4] [5] for hyposmia, and 5.6%-90.3% [2, 4, 5] for j o u r n a l p r e -p r o o f hypogeusia. however, the exact onset time and the duration of hyposmia and hypogeusia are rare reported. neurosensory dysfunction of patients with covid-19 might be considered less harmful than typical symptoms (fever, cough, or shortness of breath) [6] . however, that did not mean it should be neglected. to clarify the onset time and duration of these symptoms will offer help for early diagnosis and accurate management of in this study, we report the characteristic neurosensory dysfunction in 44 of 86 patients with covid-19. we detailly clarified the exact time of onset and duration of neurosensory dysfunction, using the chronological analysis method. the viral load of oropharyngeal swab tests was analyzed. eighty-six confirmed cases of covid-19 (admission date from march 16 to april 12, 2020) at guangzhou eighth people's hospital in guangdong, china, which was the designated hospital exclusively for covid-19 in guangzhou, were included in this study. the confirmed criteria followed the latest diagnosis and treatment guidelines for covid-19 that issued by the national health committee of the people's republic of china [7] . this study was performed in accordance to the principles of the declaration of helsinki and was approved by the ethics committee of guangzhou eighth people's hospital. verbal consent was obtained from patients before the enrollment. demographic information, clinical characteristics (included medical history, comorbidities, signs and symptoms), and laboratory findings were obtained from the j o u r n a l p r e -p r o o f electronic medical record system of guangzhou eighth people's hospital and analyzed by three independent researchers. neurosensory symptoms were obtained at the day of discharge using self-made questionnaire. the onset date was defined as the day when any symptoms were noticed by the patients. the method of chronology (a chronology is an account or record of the times and the order in which a series of past events took place) was used for analysis. oropharyngeal swabs were collected and placed into a sterile tube containing rna preservation solution. the swabs were sent for sars-cov-2 rna extraction and detection within 1 hour by a real-time reverse transcriptional polymerase chain reaction (rt-pcr )system by following the commercial test kit instructions (da'an gene cooperation, cat da0930) as previously described [8] . briefly, two pcr primer and probe sets targeting orf1a/b and ncov-n genes were separately added into the same reaction tube. positive and negative controls were involved for detection. cycle threshold (ct) values were used to quantify the viral load, with lower values indicating higher viral load. the samples were defined as viral positive when either or both genes of ct value < 41. continuous variables were described as medians and range values. the analyses were carried out using graphpad prism 9 or ibm spss statistics 25. categorical variables were compared using the fisher's exact test and continuous variables with the mann-whitney u test. spearman's correlation test was performed to analysis relationship between age and viral load, as well as between days after symptom onset and test values. the significant level was set as 0.05. shown in table 1 . the median age of patients was 25.5 years (range 6-57). 85 patients were with mild covid-19 and 1 was severe case. 18 (20.9%) patients had at least one comorbidity: chronic liver diseases (8, 9 .3%), hyperlipidemia (3, 3.5%), cardio cerebrovascular disease (3, 3.5%), followed by hypertension, anemia and hyperthyroidism (2, 2.3%). the most common typical symptom was cough (41, 47.7%), followed by fever (26, 30.2%), fatigue and pharyngalgia (16, 18 .6%), anorexia (15, 17 .4%), headache (12, 14 .0%), myalgia (8, 9 .3%), diarrhea (6, 7.0%), and vomiting (4, 4.7%); and 11 (12.8%) patients showed no typical symptoms. forty-four (51.2%) patients had neurosensory dysfunction: hyposmia (34, 39.5%), hypogeusia (33, 38.4%), and tinnitus (3, 3.5%). table 2 showed the demographic characteristics and laboratory findings of 44 cases with neurosensory dysfunction. patients with neurosensory dysfunction was noticed to have a younger age (median 23.5 years vs 31.5 years, p=0.024). of the 44 patients, 42 (95.5%) were under 40 years old (6-39 years old). neurosensory dysfunction was significantly more common in patients under 40 years old (p=0.001). women develop neurosensory dysfunction more common than men (p=0.006). there was no significant correlation between comorbidity and neurosensory dysfunction. no obvious differences in laboratory tests were noticed between patients with and without neurosensory dysfunction. a total of 407 oropharyngeal swabs were obtained from 86 hospitalized patients (mean 4.7 specimens per patient). sars-cov-2 rna was undetectable in oropharyngeal swabs from 24 patients after admission. the results showed that the viral load peaked within the first week since symptoms onset and then gradually declined; a significant negative correlation was noticed between viral load and days after symptom onset (r 2 =0.1250, p<0.001; figure 2a ). the first positive results (ct value < 41) of oropharyngeal swabs after admission was used to evaluate the initial viral load. there was no significant difference in initial ct values between patients with and without neurosensory dysfunction ( figure 2b ). age group ( figure 2c ) and gender ( figure 2d) had no significant effect on initial ct values. in this study, we detailly provided the exact time of onset and duration of neurosensory dysfunction, including hyposmia, hypogeusia and tinnitus, of patients with covid-19. patients under 40 years old, as well as women, seem to be more susceptible to neurosensory dysfunction. hyposmia tends to cooccur with hypogeusia in the early stage of covid-19, even before onset of typical symptoms. most of the reports about loss of smell and taste appears in countries outside east asia, with the incidence rate of 54.2%-90.3% [3, 5, [9] [10] [11] . there are only two reports on [2] reported that hyposmia and hypogeusia accounted for 5.1% and 5.8% of hospitalized patients in wuhan, china. in the study via telephone interview by lee et al. [4] , anosmia or ageusia was observed in 15.3% patients in the early stage of covid19 . in our cohort, 44 (51.2%) showed neurosensory dysfunction, a percentage much higher than that in the two studies. the reason for this inconsistency may be that most of the patients in our cohort were imported cases who were infected with the coronavirus abroad, and as forster et al. [12] reported, the genotyping of the coronavirus may be different (potential mutations). the present study is the first to use the chronological analysis method to detailly clarify the neurosensory dysfunction of patients with covid-19. the neurosensory dysfunction tends to occur in the early stage of covid-19, even before onset of typical symptoms. the first evidence was that of the 11 patients who had no typical symptoms, 9 reported neurosensory dysfunction. secondly, the onset time of neurosensory dysfunction is close to or even earlier than that of typical symptoms. thirdly, the average duration of hyposmia and hypogeusia in this cohort was 9.09±5.74 days and 7.12±4.66 days, which was nearer to that of 7.5±3.2 days reported in spain [9] . at present, the epidemic in guangzhou has entered the final stage, and all patients were admitted to our hospital for treatment on the day of confirmation. these facts indicate that the neurosensory dysfunction may be present before sars-cov-2 is detected in the oropharyngeal swab. all the above evidence fully shows that neurosensory dysfunction can be used as a diagnostic marker of early covid-19. thus, our findings suggest adding neurosensory symptoms to the routine screening list for covid-19. the reasons why neurosensory dysfunction often occurs early are still unclear. the following two factors could be taken into consideration. firstly, high viral load in the beginning of infection may concern the development of neurosensory dysfunction. our data revealed that the viral load remained at a high level for a week since symptom onset, which coincided with the duration of neurosensory dysfunction. however, no difference was noted in viral load between patients with and without neurosensory dysfunction, suggesting that the effect of viral load on the development of neurosensory dysfunction varies. secondly, oral cavity and nasal cavity are the main routes for sars-cov-2 invasion. studies show that ace2 could be expressed in tongue epithelial cells [13] and olfactory epithelial cells [14] . these facts might lead to the early occurrence of neurosensory dysfunction. interestingly, neurosensory dysfunction seems to affect more young patients than the elderly, which is consistent with a study by lechien et al. [7] in europe. this finding may corroborate yan et al. [4] demonstrating that smell loss in covid-19 may associate with a milder clinical course. we also noticed a correlation between gender and the development of neurosensory dysfunction. there are many differences between men and women in the immune response to sars-cov-2 infection and inflammatory diseases [15] , and women are less susceptible to viral infections based on a different innate immunity, steroid hormones and factors related to sex chromosomes [15] . a study by suzuki et al. [16] found that women are more likely to suffer from postviral olfactory dysfunction in infections caused by parainfluenza, epstein-barr virus or human rhinovirus. the similar findings in sars-cov-2 infection were obtained from our data. consistent with previous reports [17, 18] , a significant negative correlation, although weak (r 2 =0.1250, figure 2a) , was noticed between viral load and days after symptom onset. the tendency suggests that the viral load is high at the initial stage of sars-cov-2 infection, and then gradually decreases after admission. sars-cov took nearly 10 days after symptom onset until peak virus load [19] . high initial virus load in covid-19 patients suggested that sars-cov-2 can be transmitted earlier and easier than sars-cov. the viral load was reduced rapidly after admission, but could rebound within 2-4 weeks (i.e., day 11, 20, 21, 23, 25 after symptom onset) (figure 2a) , and a similar rebound pattern was noticed by huang et al. [18] and by xu et al. [20] . the antivirals can act effectively on upper respiratory tract and most of lower respiratory tract, but bronchioli terminals could be hardly affected. the coronavirus particles in bronchioli terminals, as well as the virus resistance, may result in the viral rebound in the later course of treatment. the present study noted no significant difference in ct values between patients with and without neurosensory dysfunction ( figure 2b ). lechien et al. [21] reported that the viral load was significantly higher in patients with olfactory dysfunction duration <12 days compared with those with duration >12 days. they suggest that it is beneficial to perform diagnostic swabs in the first 12 days of olfactory dysfunction to avoid the risk of a false-negative result. our data may support these findings, with the fact that the viral load is gradually reduced under treatment after admission. neither gender ( figure 2d ) nor comorbidity ( figure 2e ) was noticed to have significant effect on viral load. these findings are consistent with the report by huang et al. [18] and the report by to et al. [17] . to et al. [17] reported a positive correlation between age and peak viral load. however, in this study, no difference in ct values was noticed between age groups ( figure 2c ). this inconsistency may be due to that patients in our cohort are much younger (median 25.5 vs 62 years old) and with only one severe covid-19. this study has both strengths and limitations. its major strength is the use of chronological analysis method to detailly present the exact time of onset and duration of neurosensory dysfunction. this study proves that neurosensory dysfunction could be used as a biomarker for early diagnosis of covid-19. there are two limitations. first, only 86 patients were included. it would be better to conduct a multicenter research with large sample size. besides, for patients' comfort, we did not use nasopharyngeal swabs, which could be better for assessment of viral load on olfactory mucosa. in conclusion, the present study detailly provided the exact time of onset and duration of neurosensory dysfunction, and reported the viral load of hospitalized patients with covid-19. our findings suggest that the neurosensory dysfunction can be used as a diagnostic marker of early covid-19, and should be added to the routine screening list for covid-19. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. construction. this study is performed in accordance to the principles of the declaration of helsinki world health organization neurological manifestations of hospitalized patients with covid-19 in wuhan, china: a retrospective case series study smell dysfunction: a biomarker for covid-19. int forum allergy rhinol prevalence and duration of acute loss of smell or taste presymptomatic sars-cov-2 infections and transmission in a skilled nursing facility national health commission of the people's republic of china. the guidelines for the diagnosis and treatment of new coronavirus pneumonia clinical and epidemiological characteristics of 1,420 european patients with mild-to-moderate coronavirus disease detectable 2019-ncov viral rna in blood is a strong indicator for the further clinical severity acute-onset smell and taste disorders in the context of covid-19: a pilot multicenter pcr-based case-control study self-reported olfactory loss associates with course in covid-19. int forum allergy rhinol self-reported olfactory and taste disorders in sars-cov-2 patients: a cross-sectional study phylogenetic network analysis of sars-cov-2 genomes high expression of ace2 receptor of 2019-ncov on the epithelial cells of oral mucosa expression of the sars-cov-2 entry proteins, ace2 and tmprss2, in cells of the olfactory epithelium: identification of cell types and trends with age coronavirus cov-19/sars-cov-2 affects women less than men: clinical response to viral infection identification of viruses in patients with postviral olfactory dysfunction temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study chronological changes of viral shedding in adult inpatients with covid-19 in wuhan, china clinical progression and viral load in a community outbreak of coronavirus-associated sars pneumonia: a prospective study characteristics of pediatric sars-cov-2 infection and potential evidence for persistent fecal viral shedding psychophysical olfactory tests and detection of covid-19 in patients with sudden onset olfactory dysfunction: a prospective study we declare no conflicts of interest. key: cord-340992-88t1c0zs authors: nikolai, lea a; meyer, christian g.; kremsner, peter g.; velavan, thirumalaisamy p. title: asymptomatic sars coronavirus 2 infection: invisible yet invincible date: 2020-09-03 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.076 sha: doc_id: 340992 cord_uid: 88t1c0zs while successful containment measures of covid-19 in china and many european countries have led to flattened curves, case numbers are rising dramatically in other countries, with the emergence of a second wave expected. asymptomatic individuals carrying sars-cov-2 are hidden drivers of the pandemic, and infectivity studies confirm the existence of transmission by asymptomatic individuals. the data addressed here show that characteristics of asymptomatic and presymptomatic infection are not identical. younger age correlates strongly with asymptomatic and mild infections, and children as hidden drivers. the estimated proportion of asymptomatic infections ranges from 18% to 81%. the current perception of asymptomatic infections does not provide clear guidance for public-health measures. asymptomatic infections will be a key contributor in covid-19 spread. asymptomatic cases should be reported in official covid-19 statistics. transmission of the virus by infected, albeit asymptomatic individuals has been reported since the early stages of the outbreak 8, 9 posing substantial challenges to covid-19 containment. spread of covid-19 likely occurs to a large extent through asymptomatic individuals, as these do not present at health care or testing facilities. uncertainty about the significance of asymptomatic infections is reinforced by the vagueness with which the term "asymptomatic" is used. who defines an asymptomatic case as a laboratory-confirmed infected person without overt symptoms 10 . it remains to be established how thoroughly such a person needs to be examined clinically. moreover, a distinction between asymptomatic and presymptomatic individuals is often neglected in covid-19 case definitions. a distinction between asymptomatic and presymptomatic stages can currently only be made retrospectively, after the occurrence or non-occurrence of clinical symptoms. recent evidence suggests that elevated serum/plasma lactate dehydrogenase levels may, already in early stages, be indicative of presymptomatic infections and, thus, facilitate early differentiation 11 . diagnostic imaging cannot distinguish between the two infection stages, as, surprisingly, 30% of asymptomatic individuals showed ground-glass opacities and 27% had diffuse consolidations 12 . the frequency and infectivity of asymptomatically infected persons is one of the main reasons why covid-19 has become a pandemic. evidence has pointed to the need for strict tracking and testing of all contacts, regardless of apparent symptoms 2, 11, 13, 14 . however, detection of covid-19 has long been driven by testing patients only, a practice still recommended in the eu/eea (except germany) and uk 15 . meanwhile, some countries have started to extend testing and luxembourg and the state of bavaria (germany) have announced that the entire population of 600,000 and 13 million, respectively, shall be tested to prevent a second wave. the centre for disease control (cdc) of usa recommends diagnostic tests for both symptomatic and asymptomatic individuals with known or suspected exposure to covid-19 16 , while the european centre for disease control (ecdc) proposes tests mainly for asymptomatic healthcare workers when testing facilities are underutilized 17 . since 1 april, china has responded to the emerging significance of asymptomatic infections by establishing a separate category of "asymptomatic cases" in its daily covid 19 statistics 2 . mathematical modelling clearly supports broader test strategies. a simulation applying data from the jiangsu province, china, compared epidemiological data with an estimated asymptomatic proportion of 44% and found that asymptomatic individuals can cause faster and larger outbreaks compared to imported cases 18 . another analysis indicated that 30% of asymptomatics and 50% of symptomatic patients must be isolated to achieve disease control 19 . asymptomatic infections have increasingly been recognized in family clusters with unknown index cases. the first study cluster comprised of five family members from anyang, china, who developed covid-19 symptoms and tested positive by rt-pcr after acquiring the infection from the index case, an asymptomatic visitor from wuhan who later tested positive 20 . another study with five family members from luzhou, china, described a patient who developed severe covid-19 pneumonia after attending a family reunion. apparently, he had acquired covid-19 from an asymptomatic relative from wuhan 21 . several studies have focused on determining the incidences of asymptomatic infections. on the cruise ship diamond princess with 3711 passengers, a major outbreak with 634 cases occurred after an infected asymptomatic passenger had boarded in hong kong. due to the dense living conditions and frequent passenger contacts the r0 value was initially four times higher than in wuhan 22 . the true asymptomatic proportion, defined as those who never developed symptoms, among all infected passengers was 18% 23 . similar to the diamond princess, another study of an argentinian expedition cruise ship found that 59% of the 217 passengers tested positive for covid-19; 81% of those infected were asymptomatic virus carriers 24 . in vo, the first italian city with a confirmed covid-19 fatality, the 3711 was surveyed twice. 2.6 % of the population tested positive before the lockdown and 1.2 % tested positive after the lockdown. of these, 41% and 45% were asymptomatic before and after the lockdown, respectively 25 . when screening individuals in gangelt, germany, 22% of individuals positive for covid-19 remained asymptomatic 26 . in another study of individuals re-patriated from wuhan to japan, 13 of the of 565 (2%) evacuated tested positive and 31% of those evacuated remained asymptomatic after a sufficiently long time to complete the incubation period 27 . a first nationwide population-based study from spain including 61000 participants from 35883 households concluded that one in three infections seems to be asymptomatic and emphasizes the need for maintaining public health measures, to avoid a second epidemic wave 28 . as these findings differ greatly it is difficult to accurately determine the extent of asymptomatic infections. discrepancies could result from imprecise definitions of the term "asymptomatic" or a differing understanding of "asymptomatic" in the various studies (table1). extremely high incidences could result from unintended inclusion of presymptomatic and very mild cases. the true incidence of asymptomatic infections can only be determined if close surveillance is installed and continued at least over the estimated average incubation period of at least 5 days in order not to miss a possible onset of symptoms. when assessing public health risks raised by asymptomatic covid-19 cases it is important to determine whether the infectivity varies between asymptomatic, presymptomatic and symptomatic individuals. a study of the first 243 patients in singapore revealed a proportion of 6% presymptomatic cases with transmission occurring 1-3 days before the onset of symptoms 14 . data from three chinese hospitals, including 24 asymptomatic subjects, showed whereas 9 remained asymptomatic. there was a statistically significant difference between asymptomatic and presymptomatic infection, with higher ct values in asymptomatic individuals than in presymptomatics. however, there was no significant difference in viral shedding 34 . in addition, infectivity was found to be highest roughly a day before symptom onset and it was estimated that 44% of secondary cases were infected by a presymptomatic carrier 35 . in order to ascertain an asymptomatic, who did not meet the case definition, the detection of sars-cov-2 by rt-pcr on nasopharyngeal and oropharyngeal swabs is the only currently available standard diagnosis 36 when analysing common characteristics of patients, young age often correlated with asymptomatic or mild manifestations of covid-19. among 78 patients from wuhan, china, asymptomatic individuals were younger than symptomatic patients (median age 37 vs. 56 years) 32 . in nanjing, china, of 24 initially asymptomatic subjects, 29% who never showed symptoms were significantly younger than the presymptomatic group 40 . these results are supported by the data from the cruise liner diamond princess, where of 96 asymptomatic persons 11 later developed symptoms that made them presymptomatic. the probability of turning to a presymptomatic stage increased with age 41 . in fact, a much lower prevalence of covid-19 is observed in children than in adults, with people under 18 years accounting for 5% of cases only in the usa compared to 22% in the total population 42 . of 1412 chinese children with infection, 4% and 51% were categorized as asymptomatic and mild, respectively 43 . recent evidence suggests that the entry of sars-cov-2 via the ace2 receptor is facilitated by the membrane-bound serine protease tmprss2, which primes the viral s protein for fusogenic activity 44, 45 . since tmprss2 is a gene that associates with androgen levels, a higher expression occurs in males, which provides one explanation why they are more likely to develop severe covid-19 46 . this association also applies to the distinction between preadolescents and adults and is in line with low incidences and rather mild disease courses in children 47 . since this also indicates a higher incidence of asymptomatic infections in younger people, it needs to be examined whether this group, especially children, could silently, yet efficiently, contribute to the spread of covid-19. in geneva, switzerland, 79% of all rt-pcr-positive children under 16 years of age were infected in household clusters 48 and in wuhan, china, as much as 90% of this group were infected by a family member 49 . a systematic review identified 31 household clusters, of which only 10% had paediatric index cases compared to 54% in h5n1 influenza 50 . these observations, together with evidence of lower viral loads and milder respiratory symptoms in children, have led to the conclusion that children are unlikely to be the main cause of the pandemic 51 . consequently, re-opening of kindergartens and schools has been proposed. a low attack rate among children may yet be biased, because the risk of infection is lowest for children 52 . current data from berlin, germany, did not show significant differences in viral loads between age groups, suggesting that children may be as infectious as adults 53 . neglecting the role of children in the spread of covid-19 is precarious. it is important in modelling the pandemic to undertake careful surveillance, including asymptomatic children j o u r n a l p r e -p r o o f with rates of infections assessed by serology in order to better characterize childhood infection and the role of children in transmission networks 54 . children need protection, as some become ill, although severely only in the very minority of cases. covid-19 vaccination in children may provide protection for older, unvaccinated populations. vaccination in childhood will lead to a great deal of immunity required for overall protection in any population 54, 55 . studies suggesting high incidences of transmission through asymptomatic individuals have raised hope that broad immunization of the population occurs unnoticeably. in general, about two thirds of a population must be immunized to achieve herd immunity. on 24 june 2020, the countries with highest incidences of covid-19 were the usa, brazil, russia, india and the united kingdom, with case numbers representing 0.71%, 0.54%, 0.43%, 0.03% and 0.47% of the population, respectively, thus being far from herd immunity 56 . in gangelt (germany), an event linked to carnival celebrations caused sars-cov-2 spread throughout the city and resulted in 3% of the population with positive rt-pcr results. serological screening revealed later that 16% of the population were exposed 26 . even in densely populated and severely affected areas the prevalence of anti-sars-cov-2 antibodies is still relatively low, e.g. 11% in madrid, spain 57 , 15% in london, uk 58 and 20% in new york city, usa 59 . it is still unclear whether asymptomatic infections lead to protective immunity. it was observed that, although all patients with severe and mild covid-19 experienced seroconversion during or after hospitalization, only 1 in 5 asymptomatic patients seroconverted 30 . another comparison between an asymptomatic and a symptomatic cohort showed that igg levels were significantly higher in symptomatic group 12 . however, data from two hospitals in hong kong suggest that the severity of the disease is not correlated with serum antibody levels 60 . it would not only be misleading, but dangerous to rely on silent immunization. apparently, so far only a small proportion of the population has been exposed to sars-cov-2. the current perception of asymptomatic infections does not provide clear guidance for public health measures. as asymptomatic and presymptomatic infections are not distinguishable on a first sight, they may pose a significant threat to public health during the unlocking lockdown strategies currently implemented in many countries. therefore, public health measures need to further-mandatorily and for an unforeseeable period of timeinclude sound hygiene measures and personal protective equipment to prevent spread by asymptomatic individuals. contacts of infected persons must test for covid-19, regardless of symptoms. asymptomatic cases should be reported separately in official covid-19 statistics and shifts from asymptomatic to symptomatic stages must be reported to health authorities. mass rallies and major events need further be postponed or cancelled. asymptomatic infections are an important aspect of sars-cov-2 infection and the data addressed here show that the characteristics of asymptomatic and presymptomatic infection are not identical. asymptomatic infections will be a key contributor in covid-19 spread. infectivity studies confirm the existence of transmission by asymptomatic individuals but are contradictory when comparing viral loads and virus shedding in symptomatic and asymptomatic infections. younger age correlates strongly with asymptomatic and mild infections and therefore suggests children as hidden drivers of the pandemic. however, since childhood infections are usually far below the age average in covid-19 infections, the role of children in transmission events is not yet clear. while the public health measures might be practicable in wealthy countries with well-established and rather stable health care systems, the question on how the pandemic will affect low-and middle-income countries as observed in south america or on the african continent remains still unresponded 61, 62 . the international community is obliged to pay attention to the spread of covid-19 to low-income countries, as health systems could become severely overburdened and the pandemic could continue to elude control, hitting those hardest with the least protection. all authors disclose no conflict of interest. ☒ the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. droplets and aerosols in the transmission of sars-cov-2 asymptomatic carriers of covid-19 as a concern for disease prevention and control: more testing, more follow-up clinical and transmission dynamics characteristics of 406 children with coronavirus disease 2019 in china: a review aerosol emission and superemission during human speech increase with voice loudness clustering and superspreading potential of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infections in hong kong religious tourism and mass religious gatherings -the potential link in the spread of covid-19. current perspective and future implications high sars-cov-2 attack 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severity covid-19 in children and the dynamics of infection in families sars-cov-2 infection in children children are unlikely to have been the primary source of household sars-cov-2 infections. medrxiv children are unlikely to be the main drivers of the covid-19 pandemic -a systematic review sars-cov-2 children transmission: the evidence is that today we do not have enough evidence an analysis of sars-cov-2 viral load by patient age. medrxiv herd immunity and vaccination of children for covid19 the importance of advancing sars-cov-2 vaccines in children gobierno de españa mdcei, ministerio de sanidad, instituto de salud carlos iii, consejo interterritorial. estudio ene-covid19: primera ronda estudio nacional de sero-epidemiología de la infección por sars-cov-2 en españa (ene-covid19) informe preliminar 13 de mayo de 2020 weekly coronavirus disease 2019 (covid-19) surveillance report summary of covid-19 surveillance systems amid ongoing covid-19 pandemic, governor cuomo announces results of completed antibody testing study of 15,000 people showing 12.3 percent of population has covid-19 antibodies temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study covid-19 in africa: between hope and reality preparedness is essential for malaria-endemic regions during the covid-19 pandemic all authors disclose no conflict of interest. all authors have an academic interest and contributed equally. tpv is a member of the pan african network for rapid research, response, and preparedness for infectious diseases epidemics consortium (pandora-id-net ria2016e-1609). j o u r n a l p r e -p r o o f key: cord-351740-779g8tr1 authors: khaba, moshawa calvin; ngale, tshepo cletus; madala, nomandla title: covid-19 in an hiv-infected patient. lessons learned from an autopsy case date: 2020-09-25 journal: int j infect dis doi: 10.1016/j.ijid.2020.09.1435 sha: doc_id: 351740 cord_uid: 779g8tr1 despite measures put in places to curb the spread of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) across south africa, there has been a rapid spread which caused extensive morbidity and mortality. whilst there is currently increased covid-19 associated death, autopsies on covid positive individuals are not routinely performed. an autopsy was performed on a 19 years old african patient who was recently diagnosed with human immunodeficiency virus (hiv). he presented with clinical features of sars-cov-2 which subsequently tested positive for. important histopathological findings included diffuse alveolar damage and fibrin thrombi. no superimposed infections were noted. the cause of death was attributed to covid-19. we report the first autopsy case of hiv-infected individual with covid-19 as the cause of death. the first confirmed case of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) infection was reported in china in december 2019. this viral infection has since spread across the globe with the first case reported in south africa on march 20, 2020. coronaviruses are enveloped, non-segmented, positive-sense single-stranded rna viruses. the other two that are known to cause human diseases are beta coronaviruses-severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) (1, 2) . the clinical features ranges from asymptomatic to mild symptoms such as cough, fever, dyspnoea and severe disease which leads to acute respiratory distress syndrome and death (1, 3) . older patients and individual with hypertension, diabetes and cancer are at increased risk of infection (3) . there is little knowledge on hiv/aids and its impact on the clinical outcomes in patients with . to the best of our knowledge, this manuscript represents the first published report of an autopsy performed on an hiv infected patient with cause of death attributed to covid-19. clinical features 19 years old male african patient who was referred from a local clinic with one-week history of generalised weakness, fatigue, cough and shortness of breath. he was recently diagnosed with human immunodeficiency virus (hiv) with cd4 t lymphocytes of 17 cell/ul and viral load of 1487946 copies/ml. he was not yet on anti-retroviral therapy (art). he had no other co-morbidities. on examination, his blood pressure was 95/33 mmhg, heart rate of 103 beats/minute, fever of 38,7 0 c and saturation of 95% on 40% oxygen. he was confused, pale and hypovalaemic with generalised lymphadenopathy. he had bilateral crackles on chest examination. abdominal examination revealed massive splenomegaly and hepatomegaly. he was given an intravenous stat dose of ceftriaxone and acetaminophen; and admitted to a patient under investigation (pui) ward for covid-19 suspects. the chest x-ray showed extensive bilateral infiltrates (fig. 1a) . the full blood count showed bicytopaenia with low haemoglobin and platelets of 100 x 10 9 /l; and transfused 3 units of red blood cells. the liver function tests were mildly deranged. c-reactive protein, ferritin and procalcitonin were raised. the renal function tests revealed pre-renal acute kidney injury most likely secondary to the hypovolaemia (see table 1 for investigations). despite sars-cov-2 infection, in view of the retroviral disease, pneumocystis pneumonia, bacterial pneumonia and tuberculosis could not be excluded. he was started on trimethoprim-sulfamethoxazole 1920mg 6hourly, hydrocortisone 200mg 8 hourly, azithromycin 500mg daily and enoxaparin 60mg daily. polymerase chain reaction of the nasopharyngeal swab detected severe acute respiratory syndrome coronavirus 2 (sars-cov-2). three days post admission, his confusion worsened; developed cardiorespiratory failure and died. a complete autopsy was performed in a negative pressure autopsy room with personal protective equipment (ppe), including n95 masks, eye protection, gloves and gowns. the patient's body mass index was 18.1 kg/m 2 . he was emaciated, hypovolaemic and pale with generalized lymphadenopathy. he had serosanguineous bilateral pleural effusion and ascites. the right and left lungs weighed 884g and 772g (n=360 -570g and 325 -480g) respectively. they were oedematous, firm with alternating pale and red areas (fig. 2b) . the spleen weighed 1310g (n=156) with haemorrhagic cut surface. the liver weighed 2400g (n= 1500 -1800) with pale, greasy and yellowish cut surface. the kidneys had smooth surface with good corticomedullary differentiation on cut section. the brain and heart were unremarkable. the bone marrow was pale and soft. microscopic features: sections of the lungs showed extensive oedema with bilateral diffuse alveolar damage (dad) evidenced by hyaline membrane formation (fig 1c-e) . adjacent small calibre blood vessels with fibrin thrombi were noted (fig 1f) . granulomatous inflammation or infectious pathogens were not seen. the spleen was poorly preserved; however, infectious pathogens or neoplastic infiltrate were not seen. sections of the liver showed microvesicular steatosis and lobular inflammation. the heart, brain and bone marrow were unremarkable. the kidney, lymph nodes and pancreas were poorly preserved. the well preserved glomeruli did not show features of hypertension, diabetes mellitus or hiv associated nephropathy. furthermore, fibrin thrombi were not seen within the glomerular capillaries. the final cause of death was sars-cov-2 (covid-19) infection in hiv infected patient. much as performing autopsies on covid-19 positive individuals is still not routinely perfomed due to safety reasons, there has been a recent increase in covid-19 autopsy. the spectrum of pathological findings has emerged from this. the most consistently described autopsy findings are diffuse alveolar damage with associated desquamation of pneumocytes, oedema and capillary congestion (1). increased intra-alveolar macrophage and enlarged, atypical pneumocytes have also been seen in advanced disease (4). vascular microthrombi are seen in areas of diffuse alveolar damage with diffuse endothelial damage. whilst this feature is not pathognomonic for covid-19, it has been postulated to be specific to covid-19 as this is not a normal finding in dad (4,5). luca carsana et al. found that fibrin thrombi of small vessels were observed in 87% of lung cases and high levels of d-dimers in the blood (1) elevated d-dimers is associated increased thrombin generation in covid-19 (6) . the existence of fibrin thrombi and high serum levels of d-dimers may explain the severe hypoxaemia that indicate acute respiratory distress syndrome in these patients (1) . d-dimer levels of >1 μg/ml is associated with increased mortality in covid-19 patients (6) . in accord to what is already published, the lung findings on the index patient showed early phase of diffuse alveolar damage with associated microthrombi which is seen in covid-19. the lung findings on this patient was not different from the ones reported on non-hiv infected patient. little is known of the interaction between hiv infection and sars-cov-2 pathogenesis. furthermore, there's little knowledge on the impact of hiv infection on the clinical outcomes of patients infected with sars-cov-2. whilst hiv infected people on treatment with normal cd4 count and low viral load may not be at a high risk of serious illness, the presence of other chronic conditions may increase their overall risk (7) the fact that sars-cov-2 can cause transient immune deficiency, it denotes that hiv and covid-19 interaction may have adverse immunological and clinical outcomes. therefore, defective cellular immunity in hiv infected patients may be paradoxically protective for severe cytokine dysregulation in patients with covid-19 (8) . the index patient's clinical emaciation suggests that the low cd4 count was pre-covid-19. shalev et al hypothesized that the absence of t-cell activation alleviates the severe immunopathological phenomena seen in covid-19. while his study had its limitation, he further suggested that sars-cov-2 does not act as an opportunistic pathogen in patients with uncontrolled hiv or aids (3). tuohy et al suggested that hiv status did not significantly impact clinical outcomes in patients with sars-cov-2 infection, albeit he detected trends suggestive of worse course outcome in hiv-positive patients (9) . although the index patient was hiv infected, he was young without comorbidities. he had lymphopaenia and was not yet on antiretroviral therapy. this is contrary to the few published cases which show that high mortality rate of covid-19 in hiv infected patients is usually associated with older patients (> 50 years) with diabetes, hypertension, etc. furthermore, in view of the index patient's low cd4 count, secondary or opportunistic infection such as tuberculosis, pneumocystis pneumonia or cryptoccocal infection would be expected. however, there was no superimposed infection identified on lung sections examined. this further favoured covid-19 as the sole cause of death in this patient. with its own limitation, this autopsy has not shown any distinct pathological findings specific to hiv infection in contrast to what is already described in non-hiv infected patients. in lieu of this, more studies regarding hiv and covid-19 association are warranted as typical clinicopathological findings may likely have important treatment implications for these patients. the autopsy was done seven days after he demised, awaiting a written informed consent from the family. hence some of the organs were autolysed. mck, tcn and nm conceptualised the report and wrote the manuscript. all authors have read and approved the submitted version of this manuscript. all materials and data described in this manuscript are available upon reasonable request to the corresponding author, and if complying with patients' privacy. written informed consent was obtained from the patients' parents for scientific publication of this case report. sefako makgatho health sciences university research ethics committee (smurec) approved the publication of these case series. smurec/m/215/2020 no funding was secured for this study. the authors declare that they have no conflicts of interest the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. legends fig 1: a , chest x-ray shows extensive bilateral infiltrates with left pleural effusion; b, firm lung with alternating red and pale areas, and oedema. no visible thrombus; c -e, diffuse alveolar damage with hyaline membrane formation ( ); f, small vessels with fibrin thrombi ( ). j o u r n a l p r e -p r o o f articles pulmonary post-mortem findings in a series of covid-19 cases from northern italy : a two-centre descriptive study clinical characteristics and outcomes in people living with human immunodeficiency virus hospitalized for coronavirus disease articles pulmonary and cardiac pathology in african american patients with covid-19 : an autopsy series from new orleans articles histopathology and ultrastructural findings of fatal covid-19 infections in washington state : a case series hematologic parameters in patients with covid-19 infection clinical features and outcomes of hiv patients with coronavirus disease 2019 covid -19 in people living with human immunodeficiency virus : a case series of 33 patients outcomes among hiv-positive patients hospitalized with covid-19 we thank ms b ngubeni and nhls management for motivation and support all research endeavours. j o u r n a l p r e -p r o o f key: cord-330136-o8df8szx authors: fan, hua; zhang, lin; huang, bin; zhu, muxin; zhou, yong; zhang, huan; tao, xiaogen; cheng, shaohui; yu, wenhu; zhu, liping; chen, jian title: cardiac injuries in patients with coronavirus disease 2019: not to be ignored date: 2020-05-11 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.024 sha: doc_id: 330136 cord_uid: o8df8szx abstract objective to describe the clinical features of coronavirus disease 2019 (covid-19). methods we recruited 73 patients with covid-19 [49 men and 24 women; average age: 58.36 years (sd: 14.31)] admitted to the intensive care unit of wuhan jinyintan hospital from december 30, 2019 to february 16, 2020. demographics, underlying diseases, and laboratory test results on admission were collected and analyzed. data were compared between survivors and non-survivors. results the non-survivors were older (65.46 [sd 9.74] vs 46.23 [12.01]) and were more likely to have chronic medical illnesses. non-survivors tend to develop more severe lymphopenia, with higher c-reactive protein, interleukin-6, d-dimer, and hs-troponin i(hs-tni) levels. patients with elevated hs-tni levels on admission had shorter duration from symptom onset to death. increased hs-tni level was related to dismal prognosis. death risk increased by 20.8% when the hs-tni level increased by one unit. after adjusting for inflammatory or coagulation index, the independent predictive relationship between hs-tni and death disappeared. conclusions cardiac injury may occur at the early stage of covid-19, which is associated with high mortality. inflammatory factor cascade and coagulation abnormality may be the potential mechanisms of covid-19 combined with cardiac injury. the outbreak of the viral pneumonia caused by the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (sars-cov-2), occurred in wuhan, china in december 2019, and spread rapidly worldwide (wuhan municipal health commission,2020 ,who,2020a ,holshue ml. et al.,2020 .the illness progression in some patients was rapid. in april 27, 2020, the cumulative number of patients with infections worldwide reached 2 878 196; of these, 198 668 patients have died (who,2020b) . 4 in january 30, 2020, the world health organization issued a global warning about the highly contagious disease (who,2020c) , which was named as coronavirus disease 2019 in february 11, 2020 (who,2020d . however, there have been a few studies on the clinical characteristics of the mortality cases due to the small sample size. to understand the clinical characteristics of covid-9, we aimed to analyze the clinical features of 73 patients diagnosed with covid-19 . this retrospective study analyzed 73 patients with covid-19 who were admitted to the intensive care unit (icu) of wuhan jinyintan hospital from december 30, 2019 to february 16, 2020. the hospital specializes on infectious diseases and was prescribed by the chinese government as one of the first designated treatment units for patients with the j o u r n a l p r e -p r o o f 3 disease. the diagnosis of confirmed and clinical cases was made following the guideline of diagnosis and treatment of novel coronavirus pneumonia (trial version 5)(national health commission of the people , s republic of china,2020). this study was approved by the ethics committee of wuhan jinyintan hospital (ky-2020-28.01), and all relevant personnel waived the requirement for obtaining patients' informed consent due to the particularity of the disease outbreak. this retrospective analysis was based on the case reports, nursing records, laboratory test results, and imaging findings of the patients. the patients' data on admission, including demographics, underlying diseases, and laboratory test results were collected. two experienced clinicians reviewed and summarized the data. the patients were categorized into the non-survivors and survivors. cardiac injury was defined as blood levels of cardiac biomarkers [hs-troponin i (hs-tni] above the 99th percentile of the upper reference limit，regardless of new abnormalities in electrocardiography and echocardiography. we presented the continuous measurements with normal distributions as mean (standard deviation [sd]), whereas those that without normal distributions were expressed as median (interquartile range [iqr] ). categorical variables were described as frequency rates and percentages (%). for the laboratory test results, we also evaluated whether the data were outside the normal range. spss (version 24.0, ibm co., armonk, ny, usa) was used for all analyses.first,we compared the clinical and laboratory data between the page 6 of 21 j o u r n a l p r e -p r o o f 4 non-survivors and survivors.then the non-survivors were divided into two groups based on cardiac injury and compared the course-related data.the mann-whitney u test or student's t test was used for continuous variables, and the chi-squared test was used for categorical variables. to explore the relationship between cardiac injury and prognosis of covid-19, multivariable analysis was conducted using logistic regression models with identified factors and previously recognized risk factors. model 1 included sex and age as covariates. model 2 was adjusted by model 1 variables plus days from onset to admission.further, ck-mb+cvd history (model 3), crp+il-6 (model 4),pt+d-dimer (model 5) were entered in model 2 as a covariate respectively.a p value <.05 indicated statistical significance. among the 73 patients, 49 were men and 24 were women, with an average age of 58.36 years (sd 14.31), ranging from 24 to 79 years. many patients have chronic medical illnesses, including hypertension (32.88%), cardiovascular and cerebrovascular diseases (9.59%), diabetes (16.44%). compared with survivors, the non-survivors were older (65.46 [sd 9.74] vs 46.23 [12.01]) and were more likely to have chronic medical illnesses. the median time from symptom onset to hospital was 10 days(iqr 8-12) and 8 days (iqr 7-10) in the non-survivors and survivors, respectively (table 1) . page 7 of 21 j o u r n a l p r e -p r o o f 5 results of routine blood and biochemical examinations as well as inflammatory markers on admission of the patients were collected. on admission, most patients had marked lymphopenia, but non-survivors tend to develop more severe lymphopenia. c-reactive protein (crp) and interleukin-6 (il-6) levels were higher in non-survivors than in survivors. in our cohort, the level of d-dimer increased in 28 (38.36%) patients, and the level of d-dimer was higher in non-survivors than in survivors(1.51[0.80-7.18] vs 0.52[0.31-1.12]). in the non-survivor group, the proportion of patients with hs-tni level above the normal range was 25.53% (n=12), which was significantly higher than that of the survivor group. liver and kidney injuries on admission were not significantly different between the two groups (table 2) . on admission, the level of hs-tni increased in many patients. the level of hs-tni was 16.6(10.1-40.8) pg/ml in non-survivors, which was higher than that of the survivors. besides, hs-tni levels increased more markedly with increasing age. 40 non-survivors had test result of hs-tni，they were divided into two groups based on cardiac injury，further analysis revealed that non-survivors with elevated hs-tni levels on admission had shorter duration from symptom onset to death, and tni elevation was related to the dismal prognosis. typically, the death risk increased by 20.8% when the hs-tni levels increased by one unit. adjusted for sex,age and days from onset to admission or ck-mb+cvd, hs-tni was still the independent predictive factor for death.however, after adjusting for inflammatory index or coagulation index, the independent predictive relationship between hs-tni and death disappeared (tables 3 and 4 and fig. 1 ). covid-19 is an infectious disease that has not been comprehensively understood so far. therefore, it is of great clinical significance to explore the clinical features and factors influencing prognosis of covid-19 patients. however, studies on cases with severe covid-19 are few at present. this study enrolled covid-19 patients, including 47 non-survivors and 26 survivors, admitted to the icu. according to our results, older patients with concurrent chronic diseases have an increased mortality risk, which was consistent with the results of chen et al. (2020) . the mortality of critically ill covid-19 patients is high, but its mechanism is not clear at present, and it might be related to the virus-induced acute lung injury, inflammatory factor storm. we collected the laboratory results of patients on admission and found that 29 (61.7%) patients in the non-survivor group had elevated il-6 levels on admission, suggesting the presence of severe inflammatory response in these patients. some studies reported that the risk of respiratory failure in patients with il-6 level >80 pg/ml increases 22-folds compared with the patients with low il-6 levels(t. herold,2020) . actemra, an il-6 antagonist, is verified to block the inflammatory factor cascade to prevent the progression to severe and critical conditions and to reduce the mortality risk. similarly, there was also a marked difference in the crp level between non-survivors and survivors, suggesting that severe inflammatory response might be one of the causes of death. the lung is the major target organ of covid-19, but severe cases are mostly combined with multiple organ dysfunction. wang et al. (2020) discovered that approximately 7.2% of patients had concurrent cardiac injury, whereas the incidence rate 7 of cardiac injury was even higher among icu patients, which was approximately 22.2%. according to a study enrolling 416 subjects, the incidence rate of cardiac injury is approximately 19.7%, and concurrent cardiac injury is an independent risk factor of death. our study discovered that the level of hs-tni increased in many patients on admission, indicating that cardiac injury occurred in the early stage of the disease.the incidence rate of cardiac injury among patients at admission was 16.44%, with the non-survivors having an incidence rate of as high as 25.53%. in addition, no obvious liver or kidney dysfunction was detected, revealing that severe covid-19 patients might develop cardiac injury at the early stage of the disease, and that the heart might be the first affected extrapulmonary organ. moreover, we found that the incidence rate of cardiac injury increased with increasing age. further analysis revealed that the elevated hs-tni levels was closely correlated with the prognosis andmortality risk of covid-19 patients. specifically, the mortality risk increased by 20.8% when the hs-tni level increased by 1 unit. patients with elevated hs-tni levels on admission had a shorter duration from symptom onset to icu admission for further rescue interventions and shorter overall course of disease. at present, the mechanism of cardiac injury in covid-19 patients remains unclear. both, the novel sars-cov-2 and sars virus in 2003 belong to the β coronavirus, and ace2 has been verified as the common pathogenic target. ace2 is extensively expressed in myocardial cells, cardiac fibroblasts, and coronary artery endothelial cells; therefore, sars-cov-2 may act on ace2 to induce myocardial damage. furthermore, the recently published autopsy results of covid-19 patients demonstrated the presence of sars-cov-2 particles in the myocardial interstitium (tavazzi g et al.2020) . shi et al.(2020) discovered j o u r n a l p r e -p r o o f 8 that covid-19 patients with concurrent myocardial damage had markedly elevated inflammatory index levels, and myocardial damage was considered to be related to the inflammatory response. zheng et al.(2020) found that the d-dimer level of >0.5 µg/l was associated with a poor prognosis in covid-19 patients, and the possible mechanism could be increased production of pro-inflammatory factors in covid-19 patients, which aggravated the formation of atherosclerotic plaques and resulted in plaque rupture caused by local inflammation, pro-coagulant factors ,and hemodynamic changes, thereby inducing thrombosis and myocardial infarction. our data showed that the elevated troponin level was related to a poor prognosis, but after adjusting for inflammatory factors and coagulation indexes, the independent predictive relationship between hs-tni and death in the multivariate analysis disappeared, revealing that cardiac injury might be related to the inflammatory response and abnormal coagulation function, which was consistent with previous research results. the abovementioned findings reveal that the heart is the potential target of sars-cov-2, which is associated with the severe course of the disease; thus, early monitoring and assessment of cardiac injury should be conducted as soon as possible while paying attention to the pulmonary injury. this study has some limitations. first, the sample size was small. second, only the assay indexes upon admission were examined, whereas the dynamic changes in these indexes were not observed. therefore, larger studies are warranted to further determine the clinical features of covid-19 patients.  cardiac injury may occur at the early stage of covid-19.  cardiac injury is associated with high mortality.  inflammatory factor cascade may be a potential mechanism of covid-19.  coagulation abnormality may be another potential mechanism of covid-19. association of cardiac injury with mortality in hospitalized patients with covid-19 in wuhan, china myocardial localization of coronavirus in covid-19 cardiogenic shock level of il-6 predicts respiratory failure in hospitalized symptomatic covid-19 patients clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan, china novel coronavirus -china who.coronavirus disease 2019 (covid-19) situation report-98.accessed who.novel coronavirus(2019-ncov) situation report-11.accessed key: cord-338576-gh1plurq authors: regen, francesca; eren, neriman; heuser, isabella; hellmann-regen, julian title: a simple approach to optimum pool size for pooled sars-cov-2 testing date: 2020-08-28 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.063 sha: doc_id: 338576 cord_uid: gh1plurq systematic, large-scale testing of asymptomatic subjects is an important strategy in the management of the sars-cov-2 pandemic. in order to increase the capacity of laboratory-based molecular sars-cov-2 testing, it has been suggested to combine several samples and jointly measure them in a sample pool. while saving cost and labour at first sight, pooling efficiency depends on the pool size and the presently experienced prevalence of positive samples. here we address the question of the optimum pool size at a given prevalence. we demonstrate the relation between analytical effort and pool size and delineate the effects of the target prevalence on the optimum pool size. finally, we derive a simple-to-use formula and table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. table that allows laboratories performing sample pooling to assess the optimum pool size at a presently experienced target prevalence rate. an efficient diagnostic pipeline is crucial in the management of the present sars-cov-2 pandemic and of great value for society returning back to normality at confidence (koo et al., 2020) . recently, hogan et al. (hogan et al., 2020) have demonstrated sample pooling in sars-cov2-testing to increase capacities of rt-pcr, which remains gold standard for testing. despite compromised sensitivity, pooling may be particularly suited for testing of asymptomatic carriers with high viral load, who likely contribute most to the spreading of the disease (wolfel et al., 2020 , zou et al., 2020 . however, the decision to setup a pooling strategy with possibly compromising sensitivity must be rational and the benefits must be significant to justify the procedure of sample pooling. several critical aspects such as the setting (e.g. j o u r n a l p r e -p r o o f hot spot screening), the purpose (e.g. risk assessment), availability of equipment and materials but also local statutory provisions may affect the individual decision of a lab to setup a pooling strategy. on the other hand, the success of pooling depends on the frequency of positive samples, which also determines the optimum pool-size for a pooling strategy. positives pools must eventually be resolved which brings about additional workload. here we provide a simple strategy to estimate the optimum pool size for a two-staged pooling based on a known target prevalence. all calculations, including deriving the function that defines the required tests at a given prevalence, generation of data matrices and preparation of contour plots were performed using matlab 2019, ver. 9.7.0, mathworks inc. while the mathematical relation between a target prevalence and the resulting total number of tests required to resolve all positive subjects in a two-step pooling procedure is described in the results section, the differentiation was accomplished using the matlab "diff" function, which can be used to approximate partial derivatives. plotting of the results was achieved by generating grid coordinates as required using the matlab "meshgrid" function, then generating a matrix by applying the grid coordinates to the respective equation and eventually plotting isolines using the matlab "contour" function. intersections of the isolines of the derivative with the x-axis were used for curve fitting using the matlab curve fitting toolbox and the "power" fit algorithm. the most important factor for determining the efficiency of a pooling strategy is the net analyses required per specimen (θ), which may also be considered a proxy of associated analytical efforts and cost. while the probability pn of a pool of size ps being negative at target prevalence (p) can be described as = (1 − ) , the probability of a pool being positive (pp) can be described as this simplifies as the optimum pool size for a given frequency is defined by the local minima of the isolines in figure 1a and can be more precisely determined by the first derivative of equation 1 results from our analysis clearly demonstrate the relation between target prevalence rates and optimum pool sizes in a two staged pooling strategy. the power function (equation 2) derived from the relation between prevalence and optimum pool size ( figure 1d ) provides a simple tool to calculate the optimum pool size at an expected prevalence. our results suggest that at high target prevalence rates (>0.1), sample pooling can only marginally improve testing capacities, whereas pooling at rather low target frequencies as observed by hogan and colleagues (hogan et al., 2020) , may substantially enhance sample throughput and thus lower the effort and cost associated with rt-pcr-based testing strategies. rational pooling may thus provide the basis to overcome a shortage of reagents or help with otherwise j o u r n a l p r e -p r o o f limited testing capacities, even with larger pool sizes when used in combination with sensitive assay procedures (lohse et al.) . while sample pooling can generally increase throughput, reduce analysis time, and cost on the one hand, it may compromise sensitivity for samples with low viral loads. on the other hand, it is widely accepted that subjects with high viral loads contribute most to the spreading of the disease. this suggests pooling as a strategy towards a fast and efficient testing procedure of asymptomatic cohorts and highlights the need to adjust the pool size to an individual testing environment. while our approach can help to determine the most economical pool size at a given prevalence, there are other important aspects including but not limited to reagent availability, local regulations, sampling options and available extraction strategies that may significantly affect the decision to perform pooling in general. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. this study received no external funding. not applicable. the authors declare no competing interests. j o u r n a l p r e -p r o o f sample pooling as a strategy to detect community transmission of sars-cov-2 interventions to mitigate early spread of sars-cov-2 in singapore: a modelling study pooling of samples for testing for sars-cov-2 in asymptomatic people virological assessment of hospitalized patients with covid-2019 sars-cov-2 viral load in upper respiratory specimens of infected patients the relation between the estimated analyses per specimen and a pool size are given for various target prevalence rates as defined by equation 1 (isolines; a). local minima suggest optimum pool sizes at the respective target prevalence rate (isolines; a). the first derivative of equation 1 allows precise determination of optimum pool sizes from the intersections of the isolines with the x-axis (b). optimum pool sizes associated with a given target prevalence are summarized for select target prevalence rates (d). the association between prevalence and optimum pool size closely follows a power function = with sufficient precision (r 2 > 0,99) and a=1.24 and b = -0.466, allowing to estimate the optimum pool size by the formula = 1.24 * −0,466 . key: cord-323455-26xi2lqf authors: albarrak, ali; alotaibi, badriah; yassin, yara; mushi, abdulaziz; maashi, fuad; seedahmed, yassein; alshaer, mohamed; altaweel, abdulaziz; elshiekh, husameddin; turkistani, abdulhafiz; petigara, tanaz; grabenstein, john; yezli, saber title: proportion of adult community-acquired pneumonia cases attributable to streptococcus pneumoniae among hajj pilgrims in 2016 date: 2018-02-21 journal: int j infect dis doi: 10.1016/j.ijid.2018.02.008 sha: doc_id: 323455 cord_uid: 26xi2lqf background: the hajj mass gathering is a risk for pneumococcal disease. this study was performed to evaluate the proportion of adult community-acquired pneumonia (cap) cases attributable to streptococcus pneumoniae among hajj pilgrims in 2016. to add sensitivity to etiological attribution, a urine antigen test was used in addition to culture-based methods. methods: adult subjects hospitalized with x-ray-confirmed cap were enrolled prospectively from all general hospitals designated to treat hajj pilgrims in the holy cities of mecca and medina. patients were treated according to local standard of care and administered the binaxnow s. pneumoniae urine antigen test. results: from august 23 to september 23, 2016, a total of 266 patients with cap were enrolled in the study, 70.6% of whom were admitted to hospitals in mecca; 53% of the cases were admitted after the peak of hajj. patients originated from 43 countries. their mean age was 65.3 years and the male to female ratio was 2:1. just over 36% of the cases had diabetes, 10% declared that they were smokers, and 45.4% of cases were treated in the intensive care unit (icu). the overall case-fatality rate was 10.1%, but was higher among those treated in the icu and in those with invasive disease. the proportion of cap cases positive for s. pneumoniae, based on culture or urine antigen test, was 18.0% (95% confidence interval 13.9–23.1%). conclusions: cap during hajj has an important clinical impact. a proportion of cap cases among hajj pilgrims were attributable to s. pneumoniae, a pathogen for which vaccines are available. additional studies to determine the serotypes causing pneumococcal disease could further inform vaccine policy for hajj pilgrims. the hajj religious mass gathering hosted by the kingdom of saudi arabia (ksa) is attended by millions of muslims annually from all over the globe (yezli et al., 2017) . the event can facilitate the acquisition and transmission of infectious agents, including those responsible for respiratory tract infection, and has been linked to both local and international outbreaks of diseases (ahmed et al., 2006; memish et al., 2015a,b; yezli et al., 2016a) . examples include meningococcal disease and influenza (salmon-rousseau et al., 2016; yezli et al., 2016a) . experience from hajj shows that the implementation of appropriate prevention measures such as vaccination can significantly reduce the incidence of disease and outbreaks associated with this mass gathering. of note is the prevention of meningococcal disease outbreaks since 2001, after the introduction of compulsory vaccination with the quadrivalent meningococcal vaccine and targeted chemoprophylaxis (yezli et al., 2016b) . streptococcus pneumoniae is a common cause of pneumonia and an important cause of morbidity and mortality worldwide (feldman and anderson, 2016; varon et al., 2010) . hajj presents many risk factors for pneumococcal disease acquisition and transmission. many pilgrims are elderly with pre-existing underlying health conditions and worship under crowded conditions that promote respiratory disease transmission and infection . crowding in particular has been associated with pneumococcal disease outbreaks (banerjee et al., 2005; mercat et al., 1991) . the acquisition and transmission of s. pneumoniae is well documented during hajj, independent of clinical status (memish et al., , 2015a , and the organism is a leading cause of pneumonia-related hospitalizations and intensive care unit (icu) admissions during the event (al-tawfiq and memish et al., 2014) . vaccines against pneumococcal disease are available and are recommended for those at risk (such as the elderly and those with underlying health conditions) in many countries, including countries in the gulf states such as bahrain, kuwait, oman, qatar, and the united arab emirates (feldman et al., 2013; tomczyk et al., 2014) . the saudi thoracic society has also recently published guidelines on pneumococcal vaccination for hajj pilgrims (alharbi et al., 2016) . however, there is no official ksa recommendation for vaccination for hajj pilgrims (saudi ministry of health, 2017) . appropriate evidence-based policies regarding vaccination for pilgrims require a better understanding of the clinical burden of the disease associated with the event (al-tawfiq and . the evidence currently available for the burden of hajjassociated pneumococcal disease is suggestive, but limited by the insensitivity of bacterial cultures as a means of diagnosing the full burden of invasive or non-invasive pneumococcal pneumonia (bartlett, 2011) . the addition of urine antigen testing for adult pneumonia patients is expected to add sensitivity to the etiological attribution, without inappropriately minimizing specificity (mandell et al., 2003) . the sensitivity and specificity of this test in the diagnosis of community-acquired pneumonia (cap) due to s. pneumoniae have been reported to be in the range of 77%-97% and 67%-100%, respectively (gutierrez et al., 2003; klugman et al., 2008; molinos et al., 2015; song et al., 2013) . the aim of this study was to evaluate the proportion of hospitalized, x-ray-confirmed cap attributable to s. pneumoniae among adult hajj pilgrims in 2016, using the urine antigen test as well as standard culture-based tests, in order to determine the clinical burden of disease associated with hajj and inform vaccination policy-making. this was a prospective case-series study conducted in hospitals in the holy cities of mecca and medina, ksa. the study was conducted over a 1-month period from august 23 to september 23, 2016 (20 dull qida to 20 dull hija 1437h in the islamic calendar) around the date of the hajj peak of september 9. the study was therefore able to capture three time periods: pre-hajj (august 23 to september 8), hajj (september 9 to september 14), and post-hajj (september 15 to september 23). patients were enrolled from all general hospitals (excluding specialty hospitals such as obstetrics and gynecology hospitals and pediatric hospitals) designated to treat hajj pilgrims. these included four general hospitals and seven temporary (holy sites) hospitals in mecca and four general hospitals in medina. the study population comprised adult pilgrim patients aged 18 years old diagnosed with x-ray-confirmed cap. for this protocol, cap was defined in accordance with the us food and drug administration (fda) (us food and drug administration, 2014) as an acute infection of the pulmonary parenchyma associated with symptoms such as fever or hypothermia, chills, rigors, cough, chest pain, or dyspnea, accompanied by the presence of a new lobar or multilobar infiltrate on a chest radiograph within 72 h of hospital admission. patients with known or suspected active tuberculosis (tb; defined as smear-positive after three acidfast bacilli tests), those <18 years old, non-hajj pilgrims, and 721 patients admitted to the study hospitals with suspected cap 190 patients excluded (not pilgrims or under 18 years of age) 247 patients excluded (did not fit the definition of cap, confirmed tb cases, refused to participate) 18 patients excluded (missing crfs, no urine test performed (missed or patient unable to provide sample)), and no culture based tests performed 266 x-ray confirmed cap cases fulfilling the inclusion criteria with crfs and urine and/or culture tests performed patients who did not consent to participate were excluded from the study. based on the above criteria, 266 patients were enrolled in the study. following informed consent, x-ray-confirmed cap patients were treated according to local standard of care and administered a urine antigen test for s. pneumoniae (alere binaxnow s. pneumoniae urine antigen test; alere, waltham, ma, usa). a case report form (crf) containing patient demographic and clinical characteristics was filled out by trained investigators (to ensure consistency across sites) for each patient using the patient's medical chart and information from the patient or a family member. a case of x-ray-confirmed cap was recorded as positive or negative for s. pneumoniae on the crf based on findings from any one of the following microbiological tests: alere binaxnow s. pneumoniae urine antigen test, culture from a normally sterile site if conducted during routine investigation (i.e., blood, bone, cerebrospinal fluid, joint fluid, pericardial fluid), culture from a respiratory specimen if conducted during routine investigation and obtained by any of the following means (us food and drug administration, 2014): (1) endotracheal aspiration in intubated patients; (2) bronchoscopy with bronchoalveolar lavage or table 1 demographic and other characteristics of the pilgrim population enrolled. number ( protected-brush sampling; (3) sputum obtained by deep expectoration. the urine antigen test was performed at the patient's bedside as soon as possible after enrolment using the alere binaxnow s. pneumoniae test as per the manufacturer's recommendation. other samples were handled and processed in the same hospital as per the hospital's standard procedures. the results of microbiological investigations were collected and recorded on the crfs once available. characteristics of the study population were summarized as frequencies and percentages for categorical variables and as means with the range for quantitative variables. the association between explanatory variables and outcomes was evaluated by chi-square test or fisher's exact test, as appropriate. in addition, odds ratios (or) and their 95% confidence intervals (ci) were calculated in multivariate analyses. all tests for significance were two-sided, and a p-value of <0.05 was considered statistically significant. all analyses were performed using ibm spss statistics version 22.0 (ibm corp., armonk, ny, usa). over the study period, 721 patients with suspected cap were admitted to the 13 hospitals included in this study. of these patients, 266 had x-ray-confirmed cap and were enrolled in the study (figure 1 ). demographic and other characteristics of the enrolled study population are shown in table 1 . patients originated from 43 countries, with the most represented being indonesia (n = 59, 22.3%), egypt (n = 27, 10.2%), and india (n = 26, 9.8%). all but one case entered ksa between august 1 and september 10, 2016. most patients were elderly males (mean age 65.3 years, range 30-90 years; male to female ratio 2:1). the majority of cases (n = 188, 70.6%) were admitted to hospitals in the city of mecca, the main site of the hajj pilgrimage, including 40 cases admitted to the four temporary hospitals at the mecca holy sites. the pattern of admission shows that the number of cases admitted to hospitals increased over the study period and that most cases of cap occurred post hajj (figure 2, table 2 ). cough and difficulty breathing were the most common symptoms and were present in 91% (n = 242) and 87.2% (n = 232) of the cases, respectively. similarly, fever and tachypnea were the most common vital sign abnormalities, recorded in 83.1% (n = 221) and 79.4% (n = 211) of the cases, respectively. at least one clinical or laboratory abnormality was recorded for 63% of cases. only 22.7% (n = 59) of cases were initially admitted to the icu upon arrival at the hospital, but 45.4% (n = 108) of cases were treated in the icu during their hospital stay. diabetes mellitus was reported by 36.4% (n = 96) of the study population, and 10% (n = 26) declared that they were cigarette smokers. only 6.6% (n = 17) of the cases acknowledged having used antibiotics in the 5 days prior to their admission, although antibiotic use was unknown in a further 44.6% (n = 115) of the cases. all but one of the 17 cases who had used antibiotics prior to hospital admission had been on a single antibiotic. one person had taken both ceftriaxone and clarithromycin prior to hospital admission. the most common antibiotics used prior to hospital admission were cephalosporins (mainly third-generation) and penicillins. culture-based methods (sterile sites or respiratory specimens) were performed in 37.6% (n = 100) of the cases, with the etiology determined in 19.0% (19/100) of these cases. s. pneumoniae was identified in 13% (n = 13) of the samples and in 6% (n = 6) of samples from normally sterile sites. other pathogens were identified in six samples, including staphylococci (n = 5) and klebsiella pneumoniae (n = 1). urine antigen tests to detect s. pneumoniae infection were performed in 93.6% (n = 249) of cap cases; 14.5% (n = 36) were positive. the overall proportion of cap cases with a positive result for s. pneumoniae (based on either culture-based tests or the urine antigen test) was 18% (n = 48). valid test results for both culture-based methods and the urine antigen test were available for 83 cases. overall, agreement in results (both negative and positive) between the two methods was figure 2 . general pattern of community-acquired pneumonia (cap) case admissions to hospitals during the study period. found in 65 cases (78.3%). based on these results, the sensitivity and specificity of the urine antigen test compared to the culturebased methods were calculated to be 8.33% and 90.1%, respectively. hospital location and treatment in the icu were significantly associated with s. pneumoniae cap cases (p = 0.01). cap patients admitted to medina hospitals were less likely to have s. pneumoniae-attributable cap than those admitted to mecca hospitals (or 0.33, 95% ci 0.14-0.80). cap patients treated in the icu were 2.88 times more likely to be s. pneumoniae cap cases than those not treated in the icu (or 2.88, 95% ci 1.37-6.08). no significant association was observed between s. pneumoniae-attributable cap and age, gender, pilgrim's country of origin, antibiotic use in the 5 days prior to hospital admission, smoking, or diabetes status (table 3) . disposition at discharge was recorded for 238 cap cases. twenty-four patients died, resulting in an overall case-fatality rate of 10.1%. the case-fatality rate among cap patients treated in the icu was nearly nine times that of non-icu patients (22.2% vs. 2.48%). the case-fatality rate among all s. pneumoniae-positive cases was 16.7%, among s. pneumoniae-positive urine antigen test cases was 10.1%, and among blood culture-positive s. pneumoniae cases was 50%. only admission to the icu on arrival and treatment in the icu were significantly associated with mortality in cap cases. patients with cap treated in the icu were over 11 times more likely to die than those not treated in the icu (or 11.23, 95% ci 3.22-39.1). this study is the first to systematically enroll cases of x-rayconfirmed cap among pilgrims during the whole hajj season and from hospitals in the two holy cities of mecca and medina, giving the best estimate of the burden of cap associated with hajj. as there was active triaging of all cases of suspected cap admitted to hospitals during hajj (due to middle east respiratory syndrome coronavirus (mers-cov) screening), the study is likely to have captured almost all cap cases admitted to hospitals. cap patients originated from a wide variety of countries with a sizable proportion being older males, which is reflective of the general population of hajj. a number of other studies have reported that pneumonia is a leading cause of hospital admission (accounting for 15-40% of hospital admissions) during the pilgrimage (al-ghamdi et al., 2003; khan et al., 2006; madani et al., 2006; shirah et al., 2017) . however, most of these studies were limited to mecca city alone, specific hospital(s), or to the hajj rituals days only or a few days around that period. hence, previous studies have likely underestimated the true burden of hajj-associated pneumonia. it was found that 18% of hospitalized x-ray-confirmed cap cases among adult hajj pilgrims in 2016 were attributable to s. pneumoniae. the organism is commonly isolated from hajj pilgrims treated in clinics or hospitals during their pilgrimage. several studies have found s. pneumoniae to be the cause of pneumonia in up to 10% of cases during hajj (alzeer et al., 1998; asghar et al., 2011; mandourah et al., 2012; shirah et al., 2017) , while one study found that among 38 patients treated for severe cap at 15 facilities during the 2013 hajj, s. pneumoniae was found in 56%, using the randox respiratory multiplex array (memish et al., 2014) . other important causative pathogens reported in these studies have included other bacteria such as staphylococcus aureus, k. pneumoniae, haemophilus influenzae, and pseudomonas aeruginosa and viruses including human rhinovirus, influenza a virus, and human coronaviruses, as well as the fungus candida albicans. the results of this study are likely to be a more accurate reflection of the actual proportion of cap caused by s. pneumoniae during hajj, as the urine antigen test was used in addition to the standard culture-based methods. the test adds sensitivity to the etiological attribution without minimizing specificity (mandell et al., 2003) and overcomes many of the limitations and difficulties in culturing s. pneumoniae from clinical samples (bartlett, 2011) . although the test was highly specific in this study, it had lower sensitivity than that reported in other studies (mandell et al., 2003) . nearly half of the cap cases seen in this study were treated in the icu, reflecting the severity of the disease during hajj. admission to an icu was based on patient clinical assessment and the need for respiratory or hemodynamic support (arabi and alhamid, 2006) . pneumonia is a leading cause of icu admission during hajj, accounting for 22-31% of icu admissions, and is a major cause of severe sepsis and septic shock in icus during the event (madani et al., 2007; mandourah et al., 2012; shirah et al., 2017) . the case-fatality rate for cap patients in this study was 10.1%, which is within the range of rates reported for cap internationally (drijkoningen and rohde, 2014; vila-corcoles et al., 2016) . also, case fatality was higher among those admitted/treated in an icu and among those with invasive disease. this is also in accordance with other reports, including those among hajj pilgrims (drijkoningen and rohde, 2014; mandourah et al., 2012; shirah et al., 2017) , and is likely because patients treated in the icu or those with invasive disease have a more severe illness and are at a higher risk of death. most cap cases in this study were admitted to mecca hospitals, and the number of cases increased over the study period, with the highest admission rate being after the hajj rituals days. this pattern is in accordance with the hajj journey and its characteristics. most pilgrims arrive in ksa a few days (or weeks) before the hajj ritual dates and spend time in the holy cities of mecca and/or medina. during the hajj dates, all pilgrims return to mecca to perform the hajj rituals, most of which take place at the mecca holy sites. hence, the pre-hajj period is characterized by a smaller number of pilgrims, living in less crowded environments, spread across both mecca and medina, and relatively free of stressors associated with performing the hajj rituals. during the hajj dates, the maximum numbers of pilgrims are located in a small area of mecca performing physically challenging hajj rituals in crowded conditions, under both physical and environmental stressors. these conditions facilitate disease transmission and render pilgrims more prone to infection. it is likely that many cap cases admitted after hajj were infected during the hajj dates. this may explain the increase in the number of cap cases post-hajj, while the number of pilgrims in mecca and medina was decreasing. most cap cases were elderly males and many had diabetes or were smokers. although no significant association was found between these factors and pneumococcal pneumonia in this study, age, co-morbidities, and smoking are established risk factors for cap, including pneumococcal pneumonia (almirall et al., 2017; lynch and zhanel, 2009 ). the latter is a vaccine-preventable disease and the above risk factors are indications for pneumococcal vaccination in adults (tomczyk et al., 2014) . the finding that a proportion of cap during hajj was caused by s. pneumoniae, and that most of it was among individuals at risk of the disease, is significant. currently, pneumococcal vaccination is not one of the officially recommended/compulsory vaccinations in the hajj health requirements set by the saudi authorities (saudi ministry of health, 2017). although some countries have recommended pneumococcal vaccination for their hajj pilgrims (feldman et al., 2013; mathai et al., 2016; rashid et al., 2013) , an evidence-based policy requires a better understanding of the clinical and economic burden of the disease associated with hajj. this study is a first step in providing such data, by defining the burden of the disease in the hajj season using a more reliable diagnostic test for pneumococcal pneumonia. however, further studies are warranted, including accurate estimations of the incidence of the disease during the mass gathering and determining the serotypes causing the illness. this study has some limitations. it was aimed to systematically enroll all hospitalized x-ray-confirmed cap cases among hajj pilgrims during the study period. however, very early pneumonia may not be apparent on chest radiographs and may have led to the exclusion of some cases from the study. not all cap cases were investigated using culture-based methods, which are not routinely conducted by hospitals during hajj due to feasibility. some of the information collected from pilgrims was self-reported (e.g., smoking status) and hence may be subject to underreporting. also, information on the pneumococcal disease vaccination status of the cases was not collected, so it was not possible to investigate the effect of vaccination. in addition, as no accurate data on the adult population at risk during the study period were available, it was not possible to accurately estimate the incidence of cap during hajj. in conclusion, s. pneumoniae-attributable cap during hajj has an important clinical burden. further studies, including investigations of the incidence of the disease and s. pneumoniae serotypes involved in the disease, as well as the identification of the population at risk, are warranted to provide a comprehensive evidence base for appropriate policy-making regarding vaccination of hajj pilgrims. this study was funded by merck & co., inc. the study was approved by the king fahad medical city ethics committee and the institutional review board. all participants gave verbal consent before enrolment and the study was conducted in accordance with the guidelines of the ethics committee. tanaz petigara and john grabenstein are full-time employees of merck & co., inc. the other authors have no conflicts of interest to declare. health risks at the hajj pattern of admission to hospitals during muslim pilgrimage (hajj) prevention of pneumococcal infections during mass gathering the saudi thoracic society pneumococcal vaccination guidelines-2016 risk factors for community-acquired pneumonia in adults: a systematic review of observational studies tuberculosis is the commonest cause of pneumonia requiring hospitalization during hajj (pilgrimage to makkah) emergency room to the intensive care unit in hajj. the chain of life profile of bacterial pneumonia during hajj outbreak of pneumococcal pneumonia among military recruits diagnostic tests for agents of community-acquired pneumonia pneumococcal infection in adults: burden of disease pneumococcal disease in the arabian gulf: recognizing the challenge and moving toward a solution epidemiology, virulence factors and management of the pneumococcus evaluation of the immunochromatographic binax now assay for detection of streptococcus pneumoniae urinary antigen in a prospective study of community-acquired pneumonia in spain pattern of medical diseases and determinants of prognosis of hospitalization during muslim pilgrimage hajj in a tertiary care hospital. a prospective cohort study novel approaches to the identification of streptococcus pneumoniae as the cause of community-acquired pneumonia streptococcus pneumoniae: epidemiology, risk factors, and strategies for prevention causes of hospitalization of pilgrims in the hajj season of the islamic year causes of admission to intensive care units in the hajj period of the islamic year 1424 update of practice guidelines for the management of community-acquired pneumonia in immunocompetent adults clinical and temporal patterns of severe pneumonia causing critical illness during hajj consensus recommendation for india and bangladesh for the use of pneumococcal vaccine in mass gatherings with special reference to hajj pilgrims a cohort study of the impact and acquisition of naspharyngeal carriage of streptococcus pneumoniae during the hajj etiology of severe community-acquired pneumonia during the 2013 hajj-part of the mers-cov surveillance program impact of the hajj on pneumococcal transmission mass gathering and globalization of respiratory pathogens during the 2013 hajj an outbreak of pneumococcal pneumonia in two men's shelters sensitivity, specificity, and positivity predictors of the pneumococcal urinary antigen test in community-acquired pneumonia the potential for pneumococcal vaccination in hajj pilgrims: expert opinion hajj-associated infections saudi ministry of health. health requirements for travellers to saudi arabia for pilgrimage to makkah mass gathering medicine (hajj pilgrimage in saudi arabia): the clinical pattern of pneumonia among pilgrims during hajj diagnosis of pneumococcal pneumonia: current pitfalls and the way forward use of 13-valent pneumococcal conjugate vaccine and 23-valent pneumococcal polysaccharide vaccine among adults aged >/=65 years: recommendations of the advisory committee on immunization practices (acip) guidance for industry: community-acquired bacterial pneumonia: developing drugs for treatment streptococcus pneumoniae: still a major pathogen pneumococcal pneumonia in adults 60 years or older: incidence, mortality and prevention meningococcal disease during the hajj and umrah mass gatherings prevention of meningococcal disease during the hajj and umrah mass gatherings: past and current measures and future prospects an opportunity for mass gatherings health research we thank the mecca and medina regional general directorate of health affairs for their contribution to the study. key: cord-339576-0d6sa9pe authors: guallar, maría pilar; meiriño, rosa; donat-vargas, carolina; corral, octavio; jouvé, nicolás; soriano, vicente title: inoculum at the time of sars-cov-2 exposure and risk of disease severity date: 2020-06-14 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.035 sha: doc_id: 339576 cord_uid: 0d6sa9pe abstract a relationship between the infecting dose and the risk of disease severity has not been demonstrated for sars-cov-2 infection. here, we report three clusters of individuals that were exposed to diverse inoculi in madrid and overall developed divrgent clinical forms of covid-19. our data support that a greater sars-cov-2 inoculi at the time of exposure might determine a higher risk of severe covid-19. a relationship between the infecting dose and the risk of disease severity has been demonstrated for several viral infections, including influenza and sars [1, 2] . for covid-19, high viral loads either in saliva, respiratory secretions or blood have been associated with more severe illness [3, 4] . however, it remains unclear whether exposure to a greater viral inoculum could determine a higher risk for developing severe covid-19. although intuitive, it has been difficult to obtain such a dose-response data. herein we report three clusters of sars-cov-2 infection in madrid, in which infected persons experienced divergent clinical outcomes, namely severe, mild or asymptomatic. we hypothesize that distinct sizes of viral inoculum at the time of exposure could explain their different illness course. the first cluster was represented by 25 women (age range, 34 to 86 years-old) that lived in a community located on the outskirts of madrid. the house was wide (2000 m 2 ), with three floors, spacious common ballrooms and halls, high ceilings, and large rooms, as well as a big garden (1500 m 2 ). lockdown with strict stay home confinement was declared in madrid on march 14 th . the day before, the index case, a 47-year-old woman, were shopping and visiting relatives. on march 16 th she developed fever, cough, anosmia and dysgeusia. despite isolation at her room, two household members developed mild symptoms 2-3 days later and another 15 during the following two weeks. antibody tests performed on april 28 th to all 25 residents identified three additional infected asymptomatic persons, whereas four remained seronegative (figure 1) . in this cluster, low viral exposures along with social distancing would j o u r n a l p r e -p r o o f account for more benign clinical forms of covid-19, along with asymptomatic and uninfected cases. a second cluster of covid-19 was identified in a group of 12 women (age range, 53 to 85 years-old) that lived together in a flat apartment (650 m 2 ) downtown madrid. several of them admitted going outside home multiple times despite lockdown implementation. furthermore, many acknowledged poor compliance with social distancing measures. therefore, more than one index case could be expected in this site. from march 21th to 23rd, six of them developed mild to severe covid-19 symptoms and asked for medical assessment at home or nearby clinics. three developed bilateral pneumonia, being one hospitalized and requiring intensive care support. from march 25 th to april 3rd another four developed mild to severe symptoms, with one being hospitalized with bilateral pneumonia. antibody tests on april 28 th confirmed infection in all 12 residents, including two that had remained asymptomatic. in this cluster, indoor continuous viral exposure could account for a wider presentation of clinical forms of covid-19, being all residents infected. the third cluster consisted in a group of ten adults (7 male; age range, 56 to 76 years-old) that met within a small conference room (60 m 2 ) during 3 hours on march 4 th . it was ten days before the nationwide lockdown was implemented. the event was held at one health institution downtown madrid. three attenders had just arrived from rome (two) and milan (one), where they had been for a few days. all attenders were asymptomatic the meeting day and did not take any preventive measure, including setting one next to another and not wearing face masks. two days later two developed covid-19 symptoms and the rest within the next week. covid-19 was severe in at least four individuals, one being hospitalized at the j o u r n a l p r e -p r o o f intensive care unit for nearly one month. fortunately, he recovered. this cluster reminds many features of one large outbreak reported among members of a choir in the us state of washington [5] . in this cluster, a large indoor viral exposure seemed to account for infection of all attenders and development of severe clinical forms in half of them. it is worth to note that of the six major determinants of sars-cov-2 susceptibility to infection and risk for disease severity (figure 2) , the first two clusters only included women, whereas 7 out of 10 in the last cluster were male. the mean age (63.4, 66.3, 62.7 years-old, respectively) and the rate of chronic co-morbidities (roughly two thirds each group, being hypertension the most common) did not differ significantly comparing the three clusters. information on potential cross immunity with another endemic coronaviruses or genetic variants that could influence sars-cov-2 disease course was not available, but all individuals were living in madrid and were caucasian. therefore, we hypothesize that a different inoculum at the time of sars-cov-2 exposure could explain the different course of infection in these three clusters. it is intriguing that most recent sars-cov-2 infections seem to be less virulent than those that occurred earlier on the covid-19 outbreak [6, 7] . several factors might contribute to this observation, including more frequent late presentations at the beginning of the pandemic. alternatively, the new coronavirus could steadily become less pathogenic, as result of coadaptation to the human hosts [8] . however, our findings suggest that most likely it reflects the overall lower size of the inoculum in recent infections as a result of wide social distancing interventions compared to contagions that occurred earlier in the pandemic. the recognition that exposure to low viral loads is associated with mild or asymptomatic infections would favor a wisely steadily re-opening of activities. for instance, restricting indoor j o u r n a l p r e -p r o o f gatherings where superspreading events are more likely to occur will have a major impact on transmission, whereas other restrictions -on outdoor activity, for example-might be eased. promoting activities on open spaces coupled with rapid isolation of symptomatic persons (selfconfinement) and quarantine of contacts would act synergistically halting covid-19 spread and severity [9] . since overall 80% of contagions seem to have derived from only 10% of infected individuals [10] , shifting the sars-cov-2 community transmission rate (r 0 ) to less than 2 would require that less than half of the population would need to be infected for producing herd immunity ( figure 3) . in this scenario, covid-19 spreading would be expected to be controlled, even in the absence of antivirals or vaccines. our data support that keeping social distancing would be effective in reducing contagions as well as driving covid-19 to less severe forms. this information is crucial at a time when re-opening strategies are urgently needed for alleviating the harmful economic impact of prolonged lockdowns. clinical correlation of influenza and respiratory syncytial virus load measured by digital pcr initial viral load and the outcomes of sars clinical features and dynamics of viral load in imported and nonimported patients with covid-19 temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by sars-cov-2: an observational cohort study high sars-cov-2 attack rate following exposure at a choir practice -skagit county association of public health interventions with the epidemiology of the covid-19 outbreak in wuhan, china reducing risks from coronavirus transmission in the home -the role of viral load compounds with therapeutic potential against novel respiratory 2019 coronavirus impact assessment of non-pharmaceutical interventions against coronavirus disease 2019 and influenza in hong-kong: an observational study quantifying the impact of physical distance measures on the transmission of covid-19 in the uk figure 1. timeframe of sars-cov-2 infections and covid-19 disease severity in persons belonging to groups with different viral exposure key: cord-319814-tyqb473m authors: zhang, dingmei; he, zhenjian; xu, lin; zhu, xun; wu, jueheng; wen, weitao; zheng, yun; deng, yu; chen, jieling; hu, yiwen; li, mengfeng; cao, kaiyuan title: epidemiology characteristics of respiratory viruses found in children and adults with respiratory tract infections in southern china date: 2014-06-11 journal: int j infect dis doi: 10.1016/j.ijid.2014.02.019 sha: doc_id: 319814 cord_uid: tyqb473m background: the world health organization (who) ranks respiratory tract infection (rti) as the second leading cause of death worldwide for children under 5 years of age. the aim of this work was to evaluate the epidemiology characteristics of respiratory viruses found in children and adults with rti from july 2009 to june 2012 in southern china. methods: in this work, a total of 14 237 nasopharyngeal swabs (14 237 patients from 25 hospitals) were analyzed, and seven respiratory viruses (influenza virus, respiratory syncytial virus, parainfluenza virus, adenovirus, human metapneumovirus, human coronavirus, human bocavirus) were detected using pcr/rt-pcr from nasopharyngeal swabs. results: the demographic characteristics, viral prevalence, age distribution, seasonal distribution, and pathogen spectrum of the patients with rtis were analyzed. co-infection was observed in 483 specimens, but it was more common in male patients, inpatients, children, and young adults. it varied by season, being more prevalent in the spring and summer and less so in the winter. human coronavirus and human bocavirus were the most common pathogens, tending to occur in co-infection with other respiratory viruses. conclusions: this work adds to our knowledge of the epidemiology characteristics of these seven common respiratory viruses among patients with rti in southern china. the detection of the specific viral causes of infection provides a useful starting point for an understanding of illness attributable to respiratory infection, and might also provide data relevant to the development of prevention strategies. of risk factors is critical to the successful implementation of a prevention and control program. southern china is believed to be the origin of some important respiratory viruses, such as severe acute respiratory syndrome coronavirus (sars-cov) 16 and influenza virus. 17 southern china has large populations of humans and domestic and wild animals, as well as a large transient population that includes laborers and business people from different provinces of china and from other countries. the mixing of these large regional populations may favor the transmission of respiratory viruses. the prevalence and clinical presentation of human viral infections in china have been reported previously. 8, 10, [18] [19] [20] however, there are no previously published reports describing the etiology of the seven common respiratory tract viruses of inpatient and outpatient rti across the seasons among the various age and gender categories. information on rti from southern china is also sparse. to directly address this situation, nasopharyngeal swabs were collected continuously from children and adults seeking medical attention for rti from a total of 25 hospitals in southern china between july 2009 and june 2012. seven respiratory viruses were detected by pcr/rt-pcr and their epidemiological characteristics were analyzed. all research involving human participants was approved by the institutional review board of zhongshan school of medicine, sun yat-sen university, in accordance with the guidelines for the protection of human subjects. participants provided written informed consent after being briefed on the purpose of the study and of their right to keep information confidential. written consent was obtained from all study participants or their guardians. study participants had all been admitted to one of the 25 hospitals covering southern china. selection criteria included having one or more respiratory symptoms, such as headache, cough, expectoration, and pharyngodynia, combined with a body temperature above 37.5 8c. symptoms, history of illness, results of a clinical examination and laboratory tests, and demographic data were collected for each patient using a standardized form. nasopharyngeal swabs were collected according to a standard procedure, kept in viral transport medium, and stored at à80 8c prior to analysis (one swab was collected from each patient). for patients with viral infections, some additional clinical information was abstracted retrospectively from the medical treatment records. dna or rna was extracted from 200 ml of the nasopharyngeal swab specimen using the qiaamp minielute virus spin kit (qiagen). reverse transcription of virus rna was conducted using superscript iii rt (invitrogen, life technology) in order to detect rna viruses (flu, rsv, piv, hmpv, and hcov). dna samples extracted using the kit were used directly to detect dna viruses (adv and hbov). both kits were used in accordance with the manufacturer's instructions. flu (a, b, c), rsv, piv, adv, hmpv, hcov, and hbov were detected by standard pcr or reverse transcription pcr (rt-pcr), as described previously, using specific primers listed in the supplementary material table s1 , [21] [22] [23] [24] [25] and amplified products were detected using agarose gel electrophoresis. statistical analysis was performed using spss 13.0 (spss inc., chicago, il, usa). viral prevalences were compared using the chisquare test for categorical variables, and the cartogram was drawn using excel software. a p-value of <0.05 was considered statistically significant. a total of 14 237 nasopharyngeal swabs were collected from july 2009 to june 2012. in all, 7323 specimens were from outpatients and 6914 specimens were from inpatients. more specimens were collected from males than from females (ratio 1.48). the median patient age was 21 years (range 0-110 years). the number of children (age 14 years) was 6117 and the number of other patients (>14 years) was 8120. the seasonal distribution of patients sampled was 3756 in spring (january to march), 2617 in summer (april to june), 3993 in autumn (july to september), and 3871 in winter (october to december). an estimated 99.9% of eligible patients volunteered to participate. our data showed a significant difference in inpatient proportion by age, and showed the difference in sex distribution by age. they did not show the 20-30 and 50-55 years groups, and the relative numbers of male participants in other age groups were all over 50%. the clinical characteristics of the patients are listed in the supplementary material table s2 . most patients presented with symptoms of respiratory tract illness (rti), including fever (!37.5 8c; 100.0%), cough (84.1%), expectoration (42.1%), runny nose (36.4%), and sore throat (19.8%). the total rate of detection of all seven viruses for all specimens was 39.24% (5582/14 237). flu viruses were detected in 2632 specimens (18.50%), rsv in 1120 (7.86%), piv in 494 (3.47%), adv in 493 (3.47%), hmpv in 319 (2.24%), hcov in 351 (2.47%), and hbov in 180 (1.26%). the total viral detection rate (all seven viruses) for all inpatients was 40.01% (2772/6914), which was higher than that of outpatients (38.47%, 2817/7323) (chi-square = 3.937, p = 0.047). with the exception of flu, the viruses were more common in inpatients than in outpatients ( figure 1 ). the total viral detection rate (all seven viruses) was higher in male patients (40.11%, 3403/8485) than in female patients (37.95%, 2179/5742) (chi-square = 6.687, p = 0.010). the rates of detection of rsv, piv, and hmpv were higher in male patients than in female patients, and the detection rate of flu was lower in male patients than in female patients (chi-square = 19.262, p < 0.0001). there was no difference in the detection rates for adv, hcov, and hbov ( figure 2 ). a decline in the incidence of viral infections with age was observed for respiratory viruses, except for flu. the detection rates of rsv, piv, adv, hmpv, hcov, and hbov among children ( 14 years) were higher than among adults (>14 years old). the detection rates for rsv and hbov were highest among children <5 years old. the detection rate for flu was highest among patients aged 15-35 years ( figure 3 ). a combined graph for all three study years showing the monthly distribution of the seven respiratory viruses was drawn. the total detection rate of the seven respiratory viruses was highest in february (48.03%) and august (47.16%), and lowest in october (23.14%). the highest rate of rsv was detected in february (16.10%); the highest rate of hmpv was detected in march (4.30%); piv, hcov, and hbov showed the highest rates of detection in june: 7.87%, 3.68%, and 3.43%, respectively. flu showed the highest rate of detection in august (32.03%), and adv showed the highest rate of detection in december (4.38%). the total detection rates for the seven respiratory viruses in spring, summer, autumn, and winter were 44.31%, 41.15%, 41.66%, and 30.52%, respectively. the rates of detection were different during the four seasons (chi-square = 177.859, p < 0.0001). however, the detection rates in summer and autumn were similar in all four seasons, the detection rate of flu was the highest of the seven respiratory viruses, followed by rsv. the detection rate of flu was highest in autumn and there was no statistically significant difference in rates between spring/summer and summer/winter. however, the detection rate of rsv was highest in spring. the detection rate for piv was highest in summer. there was no difference in the rate of detection of piv during spring, autumn, and winter. for hmpv, the detection rates during spring and summer were higher than during autumn and winter. there was no difference between spring/summer and autumn/winter. the detection rate for hcov was lowest in autumn; there was no difference among spring, summer, and winter. the detection rate for hbov was lower in spring than in summer, autumn, and winter. the pathogen spectrum differed with patient age. the proportion of patients infected with flu increased with age, peaking in the group including age 15 years (86.31%), after which it fluctuated slightly but remained stable, and declined significantly after age 60 years. however, the rates of detection of rsv, piv, adv, hmpv, and hcov relative to the total rate of detection decreased after the patients reached adulthood, and then fluctuated only slightly until age 60 years, after which they declined significantly. rsv was the most common pathogen detected in children, accounting for 31.72% of all viruses detected in children. flu accounted for 25.91% of all the viruses detected in children. flu was the most common pathogen detected in adults, accounting for 74.97% of all viruses detected. flu was the most common pathogen detected in outpatients (68.25%). rsv was the most common pathogen detected in inpatients (31.78%). however, rsv was the most common pathogen detected in inpatient children (34.77%). flu was the most common pathogen detected in inpatient adults (81.04%), outpatient children (34.46%), and outpatient adults (42.02%). the proportion of flu infections among female cases (53.33%) was greater than among male cases (43.20%). however, there were fewer rsv, piv, hcov, and hmpv among female cases than among male cases. the pathogen spectrum also differed across the seasons. rsv accounted for a larger proportion of the total number of infections during spring (32.27%); piv, hmpv, and hbov accounted for a larger proportion during summer (12.92%, 9.01%, and 5.11%, respectively). flu accounted for a larger proportion during autumn (61.23%). adv and hcov accounted for a larger proportion during winter (11.35% and 9.99%, respectively) ( figure 4 ). co-infections occurred in 483 specimens, with detection rates of 3.39% (483/14 237) of all specimens and 9.55% (483/5057) of positive specimens. among the 483 co-infected specimens, 442 were double infections, 40 were triple infections, and one was a quadruple infection ( table 1) there were 175, 121, 113, and 74 cases of co-infection in spring, summer, autumn, and winter, respectively; the co-infection rates were 4.66%, 4.63%, 2.83%, and 1.91%, respectively (chi-square = 60.209, p < 0.0001). the co-infection rates in spring and summer were higher than in autumn and winter, and the rate of coinfection in winter was the lowest. the who ranks rti as the second leading cause of death worldwide for children younger than 5 years of age. 26 however, the influenza viruses are the only viral respiratory pathogens for which vaccines are currently available. 27 ongoing vaccine research and development are focusing on many other leading viral pathogens. [27] [28] [29] the detection of the specific viral causes of infection provides a useful starting point for an understanding of illness attributable to respiratory infection. it also provides data relevant to the development of prevention strategies. the objective of the study was to estimate the prevalence of respiratory viruses in people who presented with acute respiratory tract infections in southern china over a 3-year study period. human piv is a major cause of respiratory tract illness in infants and young children worldwide. 30 all children experience at least one piv infection by the age of 5 years, and re-infection may occur throughout life because of incomplete immunity. 31 the virus is associated with a wide variety of rtis, but most frequently with croup and pneumonia. annual epidemics of hpiv-3 infection are responsible for considerable economic losses as a result of hospitalization, medication costs, work and school absence, and mortality. however, piv infections have been less well studied compared to rsv and influenza viral infections. in the present study, piv was associated with 10.00% of all the rti hospitalizations and 15.00% of the rti in outpatient children. a study in the usa found piv infections to be associated with 11.50% of all pediatric rti hospitalizations. 32 human bocavirus (hbov) was first reported by allander et al. in 2005. 33 subsequently, hbov was reported in respiratory specimens collected from different countries and regions worldwide, [34] [35] [36] and detected in 1.50% to 8.30% of respiratory specimens from individuals with acute rti, especially young children and infants. in the present study, hbov was detected in 3.85% of all children <2 years old, who provided 78.33% of all the hbov-positive specimens. hbov infection has recently attracted attention worldwide. however, the incidence and clinical presentation of this infection varies widely, often involving co-infection with other potential pathogens. 37 such characteristics have led to debate over the role of hbov as a true pathogen. in the present study, among the 180 hbov-positive specimens, there were 66 (36.67%) co-infections with at least one other respiratory virus. elderly people have also been reported to be susceptible to hbov. a single lineage of hbov was detected among a wide age distribution of patients with acute rti. in this study, a total of 18 adult specimens were positive for hbov. the virus has also been found in stool specimens from patients with gastrointestinal illness. 38, 39 therefore, additional evidence and studies are needed throughout the world to gain a better understanding of this virus. this study adds to the knowledge of seasonal variations of respiratory viral infections in southern china. the epidemiology of respiratory viral infection was found to vary tremendously by geographical region. in temperate climates, the prevalence of these viruses is well documented as a cause of yearly winter epidemics of acute lower rtis. 40 this study clearly showed evidence of seven viruses throughout the 3-year study period. the highest rate of infection was in spring, with a peak in february (48.03%), and the lowest rates of infection were in winter, with a nadir in october (23.14%), which may be attributed to the fact that february is the coldest month in southern china. the detection rates for summer and autumn were similar and this is likely due to high humidity and a lack of significant delimitation between summer and autumn. with recent advances in the detection of respiratory agents, numerous studies have shown that some pediatric patients with acute lower rtis become infected simultaneously with multiple respiratory viruses. 41, 42 multiple viral infections have been linked in some reports to higher fever, a longer hospital stay, more frequent use of antibiotics, and an increased risk of admission to the icu. 43 however, there is no consensus regarding the effect of co-infection on the severity of disease. the effect may depend upon which viruses co-infect. 44 in the present study, 3.39% of specimens had multiple or dual infections, with a predominance of flu compared to the other co-viruses. however, in the positive specimens, the co-infection rates for hcov and hbov were higher than those of other respiratory viruses. the co-infection rates were higher in male patients, inpatients, and patients aged 14 years. the rates of co-infection were higher during spring and summer than during autumn and winter. the rates of co-infection were lowest during winter, which corresponded with the overall low detection rates in winter. ethical approval: all research involving human participants was approved by the institutional review board of zhongshan school of medicine, sun yat-sen university, in accordance with the guidelines for the protection of human subjects. participants received 'written informed consent' about the purpose of the study and their right to keep information confidential. written consent was obtained from all participants or their guardians. conflict of interest: the authors declare that they have no conflicts of interest. global burden of acute respiratory infections in children: implications for interventions estimates of world-wide distribution of child deaths from acute respiratory infections population-based surveillance for hospitalizations associated with respiratory syncytial virus, influenza virus, and parainfluenza viruses among young children medical burden of respiratory syncytial virus and parainfluenza virus type 3 infection among us children. implications for design of vaccine trials global burden of respiratory infections due to seasonal influenza in young children: a systematic review and meta-analysis global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis epidemiology of respiratory viral infections in two long-term refugee camps in kenya etiology and clinical characterization of respiratory virus infections in adult patients attending an emergency department in beijing parainfluenza virus infection of young children: estimates of the populationbased burden of hospitalization characterization of human coronavirus etiology in chinese adults with acute upper respiratory tract infection by real-time rt-pcr assays epidemiology of respiratory virus infections among infants and young children admitted to hospital in oman novel human bocavirus in children with acute respiratory tract infection epidemiology of human metapneumovirus respiratory syncytial virus and parainfluenza virus mortality attributable to 9 common infections: significant effect of influenza a, respiratory syncytial virus, influenza b, norovirus, and parainfluenza in elderly persons characterization of a novel coronavirus associated with severe acute respiratory syndrome the 1918 'spanish' flu: pearls from swine human respiratory syncytial virus in children with acute respiratory tract infections in china genetic variability of respiratory syncytial viruses (rsv) prevalent in southwestern china from 2006 to 2009: emergence of subgroup b and a rsv as dominant strains molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in shanghai simultaneous detection of influenza a, b, and c viruses, respiratory syncytial virus, and adenoviruses in clinical samples by multiplex reverse transcription nested-pcr assay simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-pcr assays characterization and complete genome sequence of a novel coronavirus, coronavirus hku1, from patients with pneumonia detection of adenoviruses in stools from healthy persons and patients with diarrhea by two-step polymerase chain reaction bocavirus infection in hospitalized children who estimates of the causes of death in children seasonal influenza vaccines the absence of enhanced disease with wild type respiratory syncytial virus infection occurring after receipt of live, attenuated, respiratory syncytial virus vaccines current status of vaccines for parainfluenza virus infections parainfluenza viruses parainfluenza virus type 3: seasonality and risk of infection and reinfection in young children molecular characterization and phylogenetic analysis of human parainfluenza virus type 3 isolated from saudi arabia cloning of a human parvovirus by molecular screening of respiratory tract samples human bocavirus infection in young children in the united states: molecular epidemiological profile and clinical characteristics of a newly emerging respiratory virus human bocavirus: a novel parvovirus epidemiologically associated with pneumonia requiring hospitalization in thailand human bocavirus in italian patients with respiratory diseases frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections human bocavirus infection in children with acute gastroenteritis in japan and thailand human bocavirus 1 and 3 infection in children with acute gastroenteritis in brazil respiratory syncytial virus infection in tropical and developing countries evaluation of viral co-infections in hospitalized and non-hospitalized children with respiratory infections using microarrays multipathogen infections in hospitalized children with acute respiratory infections dual infection of infants by human metapneumovirus and human respiratory syncytial virus is strongly associated with severe bronchiolitis multiple versus single virus respiratory infections: viral load and clinical disease severity in hospitalized children we owe our special thanks to the four collaborating institutes (the centre for disease control and prevention of guangdong province, guangzhou centre for disease control and prevention of the city, the affiliated pearl river hospital of southern medical university, and the supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.ijid.2014.02.019. key: cord-317399-693q80xo authors: al wahaibi, adil; al manji, abdullah; al maani, amal; al rawahi, bader; al harthy, khalid; alyaquobi, fatma; al-jardani, amina; petersen, eskild; al-abri, seif title: covid-19 epidemic monitoring after non-pharmaceutical interventions: the use of time-varying reproduction number in a country with a large migrant population date: 2020-08-20 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.039 sha: doc_id: 317399 cord_uid: 693q80xo background: covid-19’s emergence carries with it many uncertainties and challenges, one of which is epidemic management strategies. oman has implemented non-pharmaceutical interventions (npis) to mitigate the impact of covid-19. however, responses to npis may be different across different populations in a country with a large number of migrants like oman. this study investigates the different responses to npis assessing the use of time-varying reproduction number (r(t)) to monitor it. methods: polymerase chain reaction (pcr) laboratory-confirmed covid-19 data from oman was used from february 24th to june 3rd, 2020 and included demographic and epidemiological information. data were arranged into pairs of infector–infectee, and two main libraries of r software were used to estimate reproductive number (r(t)). r(t) was calculated for both omanis and non-omanis. findings: a total of 13,538 cases were included, 44·9% of which were omanis. among all, we identified 2769 infector–infectee pairs to calculate r(t). there was a sharp drop in r(t) from 3·7, (95% confidence interval [ci] 2·8-4·6) mid-march to 1·4 (95% ci 1·2–1·7) in late march in response to npis. then r(t) decreased to 1·2 (95% ci 1·1–1·3) late april when it rose, corresponding to the easing up of npis. comparing the two groups, the response to major public health controls was more evident in omanis in reducing the r(t) to 1·09 (95% ci 0·84–1·3) at the end of march. interpretation: use of real-time estimation of r(t) has allowed us to follow the effect of npis. the migrant population responds differently than the omani population. the emergence of a new infectious disease carries with it many challenges and uncertainties regarding its natural history, clinical course, transmissibility, and methods of control. for these uncertainties, the leading resort for control when there is no treatment or vaccine is to apply well-known strict public health measures to mitigate and prevent its spread. 1, 2 these measures were implemented by the chinese government after the reporting of 27 cases of corona virus disease-2019 (covid19) in wuhan, in china's hubei province, on the 30 th december 2019. measures, among others, included the isolation of confirmed and suspected cases and restriction of movement inside the country. 3 during two months after the appearance of covid-19, and despite the measures that were taken, international travel spread cases to 26 countries around the world, 4 after which the world health organization (who) announced the covid-19 to be a worldwide pandemic, 5 with daily cases reaching to 6,080,963 by the 1 st of june. 6 with the increasing number of cases and the introduction of multiple npis by most countries, there is a need to assess and monitor the transmissibility of the disease as a measurement of the effectiveness of control measures. the use of the effective reproduction number, rt, defined as the average number of secondary cases from a partially susceptible population per infectious cases, 7 is a universally used indicator for a control measure's effectiveness. 8 oman is a country of 4.60 million, and has a heterogeneous population with migrants constituting 41% of the population. 9 the effect of the control and the dynamics of transmission of covid-19 was expected to be different between these two populations, omanis and non-omanis. similar situations j o u r n a l p r e -p r o o f that led to increasing numbers of cases have been documented in many neighbouring countries of the gulf cooperation council, gcc, 10,11 and also in singapore. 12 the government of oman responded to the covid-19 pandemic much like most countries by implementing multiple npis in phases to control the disease beginning in mid-march 2020. examples include restricting flights from infected countries, to closing schools and commercial activities. (table 1 ). in this study, we will analyse the dynamics of covid-19 infection transmissibility in oman in the different populations (omani and non-omani) and the effects of the introduction of the nonpharmaceutical measures on disease transmissibility. the type of surveillance, whether active (proactive case finding) or passive (regular reporting by health care institutions), were also included in the data when only the passive surveillance cases were included. the basic reproductive number before mitigation starts are called r0. the reproduction number after mitigation starts, rt, is a measure of the transmissibility of the infection and defined as the average number of new infections one case can produce. 7 an rt of more than one means that the infection is j o u r n a l p r e -p r o o f spreading with more cases generated, whereas, an rt of less than 1, means that the spread of infection is decreasing. theoretically, we need information about the generation time-defined as the time period between the infection of the index and the next case. however, this information is usually difficult to ascertain, therefore, information regarding the serial interval (defined as the interval between disease onset in the index and the next case) distribution in the data is used instead. using r software, we utilised two main libraries to estimate the rt, epicontact library 14 and epiestim library. 15 the main function of the epicontact library 14 is to arrange the data and help estimating the distribution parameters of the serial interval in our data. the estimate-r function in the epiestim library 15 assumes a gamma distribution of the si and models the transmission of the infection using a poisson likelihood to calculate the instantaneous reproduction number. we arranged our line list into two parts, as required by epicontact library, 14 the main line list data and the contact data. the daily list of all new pcr-positive cases contains all the demographic and exposure data for each case, whereas, the contact data contains information about the transmission of infection between each identifier number. as case-by-case transmission data is available for many cases of the line list, we used the epicontact r library to find out the serial interval of our data and its distribution for the entire population, and classified this data by nationality. we used the serial interval distribution calculated by the epicontact library to estimate the rt for the entire population, classified by nationality, for the period between february 24 th until june 3 rd , 2020. we used the estimate_r function in epiestim library to calculate the rt given the distribution of serial interval (obtained by the epicontacts library) and incidence time series. this was done through a sliding window of 7 days using the poisson transmission model. 16, 17 the comparison between different rt between omanis and non-omanis was performed after extracting rt values from each estimate_r object and plotting the two-time series against each other. to investigate the behaviour of the transmission in different nationalities, the epidemic curve trend was investigated according to cluster/sporadic types in omani vs. non-omanis groups using geom_smooth function in a ggplot2 library. 18 all data cleaning and statistical analysis was done using r software version 3.6.3. 19 we used two r packages to estimate the time-varying reproduction number, epicontacts 14 and epiestim. 15 plots of incidence were produced using the library incidence in r software. 20 the comparison between the rt in the different groups was done using simple line plot. as of june 3 rd , 2020, a total of 13,538 pcr laboratory-confirmed covid-19 cases were included. only passive cases presented to the health institutions were included, the active surveillance cases were removed from the dataset, which totalled 1,974. of these cases, 44·9% were omanis and the majority of these were in the muscat governorate (71·1%), where oman's capital city, muscat, is located. among all cases, 2,769 infector-infectee pairs data have been identified and included in the contact dataset. the median serial interval was estimated to be 6, iqr (3) (4) (5) (6) (7) (8) (9) (10) (11) (12) (13) (14) the daily epidemic curve by date of onset for the passive laboratory-confirmed covid-19 cases classified by nationality: omanis and non-omanis is shown in (figure 1 ). the first cases registered in oman were in two women returning from a visit to iran on february 24 th . there was a doubling of cases from the middle of march to the end of may noticed in both nationality groups. analysis of the trend of rt in the different nationality groups is presented in figure 3 with the corresponding events as per table 1 . generally, there is a different behaviour of the rt trend between the two groups. the response to the major public health control phase, phase 2, was more evident in omanis in reducing the rt to 1·09 (95% ci 0·84-1·3) at the end of march. nevertheless, closure of muscat and mutrah (old market area) has a marked reduction in rt for the non-omani group reaching 0·9 (95% ci 0·8-1·1) by mid-april. whereas the number of sporadic cases not linked to a known cluster increase (figure 4 ). with the increasing numbers of covid-19 cases in oman, our study showed the feasibility of using the time-varying rt to assess and explain transmissibility dynamics and epidemic progression. we j o u r n a l p r e -p r o o f showed that there is a marked reduction in the reproduction number of covid-19 infections in oman in response to the major public health control introduced by the government. however, this reduction was not strongly evident in the non-omani group compared to the omanis. in fact, the closure of muscat (specifically the old market area) drastically decreased rt. the estimated median serial interval in our study was 6, iqr (3) (4) (5) (6) (7) (8) (9) (10) (11) (12) (13) (14) . previous studies have estimated this parameter to be 4.6 days 21 (95% cri: 3.5, 5.9) and 4.9 days (95%ci: 3.6−6.2) 22 the daily number of new cases is known to be influenced by testing capacity. however, the use of timevarying rt in assessing the transmissibility dynamics and epidemic progression was a crucial tool to know how the mitigation measures influenced rt. nevertheless, a study from china demonstrated that changes in reporting rates substantially affect estimates of rt. 23 thus, the initial rt is influenced by testing frequency, contact tracing, and reporting of mild cases outside hospital. because of these reasons, rt will fluctuate from country to country. the development of the pandemic in oman has followed the trend seen in other countries that could not curb the outbreak before the spread of covid-19 in the community. oman introduced most of the same mitigation measures implemented in most countries, stopped international travel by closing the points of entries (airports, seaports and ground crossing), closing schools and shops, sending public and private sector workers home, introducing the use of masks in public spaces, and restricted movement to districts with particular high numbers such as the old markets in muscat. a modelling study from china showed how the comprehensive package of mitigation interventions china implemented in hubei province caused the rt to rapidly decline below one in areas where npis were implemented. 24 another study based on data from wuhan, china, found that the mitigation measures reduced the median number of infections by more than 92% (iqr 66-97) and 24% (13-90) at the peak and at the post peak of the outbreak. 25 on the basis of exponential curve prediction, and the assumption that the duration of infection ranges from 15 to 20 days, a study from italy estimated the r0 to be from 2·8 to 3·3. 26 this number is similar j o u r n a l p r e -p r o o f to that reported for the initial phase of the infection outbreak in wuhan, 24 and slightly higher than 2·2 as reported by li and colleagues in a more recent report. 27 such numbers were similar to those found in our study. throughout the outbreak, the number of cases has been higher in the migrant population compared to many of the disease clusters in the omani population are present because omanis tend to live in extended families (5-12 per households), and thereby increase the possible number of contacts for each primary case. a study from the uk found that a 74% reduction in the average daily number of contacts observed per participant (from 10·8 to 2·8) would be sufficient to reduce rt from 2·6 prior to lockdown to 0·62 (95% ci 0·37-0·89) after the lockdown, based on all types of contacts. 28 another study from china also found that transmission of covid-19 was prominent in family clusters. 29 the rise in rt by the end of march was due to a considerable number (roughly 8,000) of omani students returning from abroad even though they were placed in institutional or home quarantine. one study looked at the effect of travel restrictions in china and found that the travel quarantine of wuhan delayed the overall epidemic progression by only 3 to 5 days in mainland china but had a more marked effect on the international scale where case importations were reduced by nearly 80% until mid-february. 30 the travel restrictions in oman were effective, except for food supply trucks, which continued over the border with the united arab emirates, and between the locked down governorates. the situation in oman is complicated by having two major and socio-economically different population groups, omani nationals and migrants. so far, countries with this population structure have been unable to control the outbreak as efficiently as countries with homogeneous populations, with taiwan, south korea and hong kong as prime examples. 31, 32 in singapore, the outbreak expanded rapidly once the j o u r n a l p r e -p r o o f infection spread into the dormitories for migrant workers 12 and by june 16 th , 731 cases per 100,000 population were confirmed. in qatar, another country with a large migrant population has 3,080 tested positive cases per 100,000 population since the start of the outbreak 10 while saudi arabia has reported 445 cases per 100,000 population. 11 easing mitigation efforts increased the number of cases, and it can be argued that the opening of the small businesses and shops happened too early; however, the overall situation was complex because many small shop owners and self-employed had had no income for months. nevertheless, with this transmissibility and with the way in which oman handles communicable diseases, the crude mortality rate from covid-19 in oman is still comparably low at 0·4%. isolation and contact tracing reduce the time during which cases are infectious in the community, thereby reducing the rt. the overall impact of isolation and contact tracing, however, is uncertain and highly dependent on the number of asymptomatic cases. 33 as case numbers rise, the burden of contact tracing and quarantining increases. a modelling study from the us indicates that in such a situation, emphasis should be on physical distancing and contact tracing whereas isolation should be prioritised to persons with a high risk of transmission to others. 34 an analysis of the four major clusters in south korea estimated the rt at 1·5 (95% ci: 1·4-1·6). the intrinsic growth rate was estimated at 0·6 (95% ci: 0·6-0·7), and the scaling of growth parameter was estimated at 0·8 (95% ci: 0·7-0·8), indicating sub-exponential growth dynamics of covid-19. the results indicate an early sustained transmission of covid-19 in south korea and support the implementation of social distancing measures to rapidly control the outbreak. 35 one model found that the effects of physical distancing strategies vary across age categories; the reduction in incidence is highest among school children and older individuals and is lowest among working-age adults. children are at a similar risk of infection to the general population, but less likely j o u r n a l p r e -p r o o f to have severe symptoms; hence they should be considered in analyses of transmission and control. 36 it is a limitation of this study that we did not stratify the rt into different age groups. 37 another limitation of this study is that the testing capacity increased as the pandemic progressed. using daily time series of covid-19 incidence, epidemic curves of reported cases may not always reflect the true epidemic growth rate due to changes in testing rates which could be influenced by limited diagnostic testing capacity during the early epidemic phase. 38 a third limitation of the study is the increasing number of sporadic cases by the end of the study period indicating the lagging in the identification and hence classification of the source of infection. this is likely due to the overwhelmed fatigued public health workforce in the country. there is, therefore, a call for increasing and training this workforce to be able to cope with current and future epidemics. in the short term, the introduction of advanced technologies (such as artificial intelligence and location tracking systems) will help public health professionals in this battle against covid-19. the use of real-time estimation of the rt has allowed us to follow the effect of the mitigation strategies adopted by the government. our analysis shows that the migrant population behaves differently than the nationals and that the covid-19 infection is spreading more rapidly in this population mainly because of their special living conditions. . the trend of incidence per 100,000 population (with 95% ci) of daily cases in omanis and non-omanis. after june 1 st , the number of cases that could not be linked to known clusters increased rapidly. cluster of cases: more than two cases that can be linked to a common index case. sporadic cases: cases that cannot be linked to existing clusters. 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during epidemics improved inference of time-varying reproduction numbers during infectious disease outbreaks elegant graphics for data analysis r: a language and environment for statistical computing incidence: compute, handle, plot and model incidence of dated events serial interval of novel coronavirus (covid-19) infections estimating the serial interval of the novel coronavirus disease (covid-19): a statistical analysis using the public data in hong kong from preliminary estimation of the basic reproduction number of novel coronavirus (2019-ncov) in china, from 2019 to 2020: a data-driven analysis in the early phase of the outbreak first-wave covid-19 transmissibility and severity in china outside hubei after control measures, and second-wave scenario planning: a modelling impact assessment the effect of control strategies to reduce social mixing on outcomes of the covid-19 epidemic in wuhan, china: a modelling study covid-19 and italy: what next? early transmission dynamics in wuhan, china, of novel coronavirus-infected pneumonia quantifying the impact of physical distance measures on the transmission of covid-19 in the uk household secondary attack rate of covid-19 and associated determinants in guangzhou, china: a retrospective cohort study the effect of travel restrictions on the spread of the 2019 novel coronavirus (covid-19) outbreak how south korea responded to the covid-19 outbreak in daegu response to covid-19 in taiwan: big data analytics, new technology, and proactive testing effectiveness of isolation, testing, contact tracing, and physical distancing on reducing transmission of sars-cov-2 in different settings: a mathematical modelling study comparative impact of individual quarantine vs. active monitoring of contacts for the mitigation of covid-19: a modelling study transmission potential and severity of covid-19 in south korea epidemiology and transmission of covid-19 in 391 cases and 1286 of their close contacts in shenzhen, china: a retrospective cohort study age-dependent effects in the transmission and control of covid-19 epidemics changes in testing rates could mask the novel coronavirus disease (covid-19) growth rate the authors would like to thank lesley carson for her editorial assistance in finalizing the manuscript. the authors declare that they have no conflict of interest the study was funded by the ministry of health, directorate general for disease control and surveillance as part of an operational research. the study was approved by the directorate general for disease surveillance and control, and there was no need for patients' consent as the study was anonymous and used the data produced for public health purposes. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.j o u r n a l p r e -p r o o f al jardani review & editing the manuscript,eskild petersen wrote the discussion and contributed to the overall manuscript, seif al-abri supervised the study and participated in all stages of the manuscript. key: cord-355480-mx9dbm73 authors: bajunirwe, francis; izudi, jonathan; asiimwe, stephen title: long distance truck drivers and the increasing risk of covid-19 spread in uganda date: 2020-06-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.085 sha: doc_id: 355480 cord_uid: mx9dbm73 abstract objectives to examine the patterns of covid-19 transmission in uganda. methods we reviewed press releases from the uganda ministry of health from when the first case was announced on march 22 up to may 29, 2020 a 10-week period. we obtained the press releases from the moh website and the twitter handle (@minofhealthug). data include number of persons tested and the categories classified as international arrivals, community members and long distance truck drivers. results the first cases were international arrivals from asia and europe and thereafter community cases emerged. however, in the middle of april 2020, covid-19 cases were detected among long distance truck drivers. by may 29, 2020, a total of 89, 224 persons had been tested and overall 442 tested positive. of those that tested positive, majority or 317 (71.8%) were truck drivers, 75 (16.9%) were community cases and 50 (11.3%) were international arrivals. majority of community cases have been linked to contact with truck drivers. conclusions the truck drivers are the most frequently diagnosed category, and have become a core group for covid-19 in uganda. they have generated significant local transmission which now threatens a full blown epidemic in the country unless strict controls are put in place. subgroups of the population with a higher prevalence or incidence of an infectious disease are often called core groups and can serve as a source of infection to the general population. the term has commonly been applied to sexually transmitted infections such as hiv, syphilis and gonorrhea (watts et al. 2010 , gesink et al. 2011 , lewis 2013 but can apply to non-sexually transmitted infections (lietman et al. 2018) . core groups may spread infection to the general population directly or through bridge populations, and will sustain infection levels at endemic or even epidemic levels unless control measures are instituted to lower prevalence of disease among them or restrict their contact with the general population. in december 2019, cases of a rare pneumonia, connected to a sea food market were reported in wuhan, china and the causative agent was identified as a viral agent that was named severe acute respiratory syndrome coronavirus 2 (sars-cov-2) (zhu et al. 2020) , the cause of what we now know as corona virus disease (covid-2019). starting in china, the infection spread very rapidly and has now nearly reached all continents. given the scale and rate of spread, it is clear that the sars-cov-2 is a highly infectious agent, with a relatively large basic reproductive rate estimated to be at least three j o u r n a l p r e -p r o o f (d'arienzo and coniglio 2020 , liu et al. 2020 , zhuang et al. 2020 . also, given its origin from a single country, all new cases in other countries were introduced by travellers from china and eventually to the new hotspots in asia and europe. in africa, the first case was reported in egypt in mid-february and in uganda, the first case was reported by the ministry of health (moh) on march 22, 2020, of a traveler arriving from dubai. the ministry initiated steps to screen travelers from hotspot countries and presidential directives were issued to close international borders. however, long distance trucks were allowed access to bring essential goods into the country or as transit to neighboring countries of rwanda, democratic republic of congo and south sudan. in this paper, we track the reports of new covid-19 cases reported by the moh and trace the emerging patterns of the new cases reported and identify the categories of persons at high risk for covid-19 in uganda. we reviewed moh reports and press releases for new covid-19 cases detected in uganda as they were made public on a regular basis. the reports are regularly posted on the twitter page for the ministry of health (@minofhealthug) and all entries were verified based on posts at this handle. data were entered into excel and analyzed using stata version 12. we plotted an epidemic curve using a 7-day interval as the unit on the time scale. we classify the cases into three categories namely: international traveller, local/ community cases, and long-distance truck drivers. international travellers are those passengers who arrived from a foreign country regardless of their citizenship. local cases are those that were diagnosed among local residents and had no evidence of recent foreign travel, and these were assumed to be a result of local transmission, or what the moh refers to as community cases. long distance truck drivers are those who arrived at uganda's borders as drivers of trucks carrying merchandise or goods, regardless of their nationality. we report a combination of both ugandan and foreign national cases detected in uganda and do not specify the nationalities of the cases. we tracked new cases of covid-19 detected between march 22, 2020 and may 29, 2020 a period of 10 weeks. the first case was reported on march 21, 2020. a total of 89, 224 persons were tested and overall 442 tested positive. of those that tested positive, majority or 317 (71.8%) are truck drivers, 75 (16.9%) were community cases and 50 (11.3%) were international arrivals as shown in table 1 below. table 1 the data are also shown in the figure 1 below and indicate that at the beginning of the ugandan epidemic, the cases were all international arrivals. these quickly shifted to community cases but have since mid-april been dominated by truck drivers, followed by a surge in community cases starting in mid-may. the steady rise in covid-19 cases among truck drivers has been has been accompanied by a rise in the community cases. at the beginning of the epidemic, the first 5 community cases identified were all linked to contact with international travelers. however, the subsequent community cases have all been linked to most probable contact with truck drivers. we present novel data to describe the dynamics of covid transmission in a setting where local transmission has been largely contained, but current data suggest the number of new cases could escalate. the first cases were all international travelers as described before (olum and bongomin 2020) , then community cases arising from contact with the international travelers were detected, and currently long distance truck drivers and their local contacts now dominate the epidemic, and threatening an escalation in the epidemic. these events take place in the midst of a national lockdown that was announced on march 19, 2020 and only eased on may 25, 2020. long distance truck drivers have established themselves as the highest risk group for covid-19 currently in uganda. this population has historically been at risk and formed a core group for other infectious diseases such as hiv and other stds (pickering et al. 1997 , gysels et al. 2001 ). the reasons why long distance truck drivers are likely to test positive for covid are not clear. there are some possible explanations. first, is that they drive long distances, and this exposes them to a larger social network, in most urban and likely crowded places such as trading centers, ports of goods shed where probability of mixing with infected persons may be increased. the second is that they may represent the general prevalence of the communities where they come from, signifying high prevalence in the neighboring countries. there is limited screening data from the neighboring countries to corroborate this hypothesis. the data suggest that interventions for drivers to limit social contact along their journey are urgently required. transport companies will need to test their drivers and ensure those who are positive do not proceed with the journey. uganda embarked on testing the truck drivers in mid-april and initially allowed them to continue their journey before results were available. samples were then transported to a hub in entebbe, near the capital kampala. this may have cost the country an increase in community transmission as evidenced by the growth in cases in week 9 and 10. with evidence of this increased community transmission, the moh has changed the approach to now test the drivers at border points, and truck drivers who test positive are not allowed to continue their journey. the strength of this report is that we present novel data, comprehensive to include all confirmed cases to-date as reported by moh and collected using innovative means. the limitation of this analysis is that new data are added daily and the epidemic is dynamic. data analysis should be done on a continuous basis to obtain a more complete and up-to-date picture of the epidemic trajectory. in conclusion, the covid-19 epidemic in uganda was sparked by travellers from europe and asia. the country is now facing threats of new transmission from regional long distance truck drivers arriving from neighboring countries. the epidemic is now literally being driven by the truck drivers who have emerged as a core group for covid in uganda. public health prevention measures that take into account regional integration of efforts are required to ensure success for the covid programs in uganda and its neighbors. j o u r n a l p r e -p r o o f assessment of the sars-cov-2 basic reproduction number, r0, based on the early phase of covid-19 outbreak in italy sexually transmitted disease core theory: roles of person, place, and time truck drivers, middlemen and commercial sex workers: aids and the mediation of sex in south west uganda the role of core groups in the emergence and dissemination of antimicrobial-resistant n gonorrhoeae identifying a sufficient core group for trachoma transmission the reproductive number of covid-19 is higher compared to sars coronavirus uganda's first 100 covid-19 cases: trends and lessons sexual networks in uganda: casual and commercial sex in a trading town remodelling core group theory: the role of sustaining populations in hiv transmission a novel coronavirus from patients with pneumonia in china preliminary estimating the reproduction number of the coronavirus disease (covid-19) outbreak in republic of korea and italy by 5 mar key: cord-354780-yzyixucr authors: lin, chih-yen; wang, wen-hung; urbina, aspiro nayim; tseng, sung-pin; lu, po-liang; chen, yen-hsu; yu, ming-lung; wang, seng-fan title: importation of sars-cov-2 infection leads to major covid-19 epidemic in taiwan date: 2020-06-13 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.031 sha: doc_id: 354780 cord_uid: yzyixucr abstract objective covid-19 has recently become a pandemic affecting many countries worldwide. this study aims to evaluate current status of covid-19 in taiwan and analyze the source of infection. methods national data regarding sars-cov-2 infection were obtained from taiwan cdc at the end of april, 2020. these data were subjected for analysis of the current status and correlation between indigenous and imported covid-19 cases. phylogenetic tree was performed to analyze the phylogeny of taiwanese sars-cov-2 isolates. results the initial case of sars-cov-2 infection in taiwan was detected on january 21, 2020. epidemiological data indicate that by april 30, there were a total of 429 covid-19 confirmed cases with the death rate of 1.3%. most of cases were identified as imported (79.9%; 343/429) with majority transmitted from united states of america (22.1%) and united kingdom (17.6%). results from phylogenetic tree analyses indicate that the taiwanese sars-cov-2 isolates were clustered with the sars-cov-2 isolates from other countries (bootstrap value 98%) and sub-clustered with bat sars-like coronaviruses (bootstrap value 99%). conclusion this study suggests that importation of sars-cov-2 infection was the primary risk-factor resulting in the covid-19 epidemic in taiwan. other countries (bootstrap value 98%) and sub-clustered with bat sars-like coronaviruses (bootstrap value 99%). this study suggests that importation of sars-cov-2 infection was the primary risk-factor resulting in the covid-19 epidemic in taiwan. keywords: covdi-19, taiwan, imported, indigenous short communication: emerging diseases pose a threat to global health and has the potential to become fatal. in december 2019, an atypical pneumonia prompted by a novel coronavirus, was first reported wuhan, china (huang et al., 2020) . this novel coronavirus was initially named 2019-novel coronavirus (2019-ncov), however, currently the name has been established as the severe acute respiratory syndrome coronavirus-2 (sars-cov-2); with the disease being named as coronavirus disease 2019 (covid-19) (coronaviridae study group of the international committee on taxonomy of, 2020) since the first reported case, there has been a rapid increase in the number of cases, with outbreaks being reported in countries all over the world. the sars-cov-2 has gradually disseminated to europe, america and asia via travelers and has caused a covid-19 pandemic since march (who., 2020b). the world health organization (who) declared the outbreak as a public health emergency of international concern on january 30, 2020 and an official j o u r n a l p r e -p r o o f 4 pandemic on march 11, 2020. as of april 30, 2020, more than 3.2 million cases of covid-19 have been reported in 185 countries and territories, resulting in more than 229,000 deaths (who., 2020b). coronaviruses are non-segmented enveloped viruses with a single-stranded, positive-sense rna genome. coronaviruses are known to infect a variety of animals with some strains being capable of infecting human. in recent decades, the severe acute respiratory syndrome coronavirus (sars-cov) and middle east respiratory syndrome coronavirus (mers-cov) has caused regional outbreaks, leading to high mortality in human infections (peeri et al., 2020) . in 2003, there was an outbreak of sars-cov in taiwan with 664 sars probable cases and 346 laboratory confirmed cases (taiwan taiwan is an island in the pacific ocean, located beside mainland china. international travel has an important role in the transmission of emerging or re-emerging infectious diseases in taiwan . in recent decades, the interactions between taiwan and china have become frequent and close. through this close interaction, sars-cov-2 infection was initially detected in taiwan on january 21, 2020 (taiwan cdc.) (fig.1a&1b ). this first case was a 50-year-old woman who was detected by a fever screen station in taoyuan international airport, as she arrived from wuhan, china. since then, several sporadic covid-19 cases have been detected in taiwan between january to early march, 2020 (fig.1a&1b ). data indicates that the covid-19 imported cases have dramatically increased since the middle of march (fig.1a) . before the mid of march, the incidence of covid-19 importation was 0.58 average per day. after that, the incidence of covid-19 importation increased to 10.57 average per day (fig.1b) . we j o u r n a l p r e -p r o o f further investigated the source of these covid-19 importation. our results indicated that the imported covid-19 cases were mainly from united states of america (22.1%), united kingdom (17.6%) and france (6.5%) (fig.1c ). in addition to imported cases, there were a few indigenous covid-19 cases reported. according to taiwan cdc, by the end of april, there were 429 covid-19 laboratory confirmed cases with the fatality rate of 1.39%. among these cases, 343 (79.9%) and 55 (12.8%) were identified as imported and indigenous covid-19, respectively (fig.1d ). the rest of cases (7.2%) remain questionable, as their source of infection were not clearly defined. accordingly, we suggest that the constant importation of sars-cov-2 infection is the major risk factor leading the covid-19 epidemic in taiwan. further, the source of infection from the indigenous cases were traced. results indicated that most of indigenous cases (81.8%; 45/55) had contact history or exposure to sars-cov-2 infected patients, sars-cov-2 contaminated devices or environment through a direct or indirect way (fig.1d ). there were 10 (18%) indigenous covid-19 cases that remained unclear has to their possible source of infection (fig.1d) . we further addressed the phylogeny of the sars-cov-2 isolated in taiwan. results demonstrated that three taiwanese isolates, collected in the early phase of the covid-19 epidemic, were similar with other sars-cov-2 isolates from other countries with bootstrap value of 98% (fig.2) . it was also noted that sars-cov-2 was sub-clustered with bat sars-like strains isolated from china (bat-sl-covzxc21 and bat-sl-covzc45) (bootstrap value 99%) (fig.2) , indicating that sars-cov-2 might have possibly evolved from bat sars-like viruses. however, the source and origin of sars-cov-2 still remains controversial, and further studies are demanded. to reduce the effects of covid-19 importation to taiwan, taiwan cdc has implemented relevant prevention strategies. the international airport reinforced fever screening of arriving passengers, questioning about their travel history, and conducting health assessments. travelers coming from covid-19 affected countries were required to fill out a "novel coronavirus health declaration and home quarantine notice". furthermore, foreign nationals were prohibited to enter taiwan since march 19, 2020 in response to covid-19 pandemics. the covid-19 spectrum of illness severity has been divided into four types: mild, moderate, severe, and critical (2020, gao et al., 2020 , who., 2020a . the who reported that fever, fatigue and dry coughing are considered the main clinical manifestations of covid-19 patients. other symptoms may include runny nose, myalgia, pharyngalgia, stuffy nose, and diarrhea, however, these are relatively less common (who., 2020b). in severe cases, the covid-19 may become fatal due to respiratory failure, shock and organ failure. the clinical features of covid-19 are shown in table 1 . with this novel coronavirus causing a pandemic, more and more evidences indicate that majority of the covid-19 cases may not develop to have severe manifestations with some cases even remaining asymptomatic; nevertheless, these individual still have the ability to transmit the virus to others. asymptomatic infections are identified as individuals testing positive for the detection of sars-cov-2 nucleic acid using rt-pcr (gao et al., 2020) (table 1) , however, these individuals do not display the typical clinical symptoms and there are no apparent abnormalities in their images, including lung x-ray film and computed tomography (ct). taiwan cdc indicates that around 60-70% covid-19 patients belonged to asymptomatic or mild cases (taiwan cdc.) . similar indicating that most sars-cov-2 infected patients were asymptomatic. the reasons for majority covid-19 infections displaying "none-to-mild symptom" remain unclear. it has been proved that sars-cov-2 invades cells by using angiotensin-converting enzyme 2 (ace2), as its receptor (zhou et al., 2020) . expression of lower level of ace2 or weaker binding capacity between sars-cov-2 and ace2 should be an essential factor that leads to the absence of any clinical manifestations for asymptomatic infections. in addition, host major histocompatibility complex (mhc) is also proposed to play a certain role to mildly initiate and regulate the sars-cov-2 induced immunopathogenesis (nguyen et al., 2020) . it is suggested that more clinical samples should be collected and a comparative examination of ace2 as well as mhc typing should be carried out. here, we report the current status of covid-19 epidemic in taiwan. we found that importation of sars-cov-2 infection was the major risk factor correlating with the outbreak causing a threat to taiwan. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. the phylogenetic tree was constructed on the basis of nucleotide sequence of full-length genome (~29kb). the filled red circles indicates taiwanese sars-cov-2 isolates. analysis was performed by using mega 6 software and neighbor-joining method. bootstrap support values > 70 are shown (1,000 replicates). j o u r n a l p r e -p r o o f (3) complicated with other organ failure positive j o u r n a l p r e -p r o o f coronaviridae study group of the international committee on taxonomy of v. the species severe acute respiratory syndrome-related coronavirus: classifying 2019-ncov and naming it sars-cov-2 a systematic review of asymptomatic infections with covid-19 clinical features of patients infected with 2019 novel coronavirus in wuhan, china the sars, mers and novel coronavirus (covid-19) epidemics, the newest and biggest global health threats: what lessons have we learned? imported dengue fever and climatic variation are important determinants facilitating dengue epidemics in southern taiwan clinical management of severe acute respiratory infection (sari) when covid-19 a pneumonia outbreak associated with a new coronavirus of probable bat origin rr (respiratory rate) spo2 (blood oxygen saturation levels) these data were referenced with previous publications the authors wish to thank the staff from center for tropical disease control for their assistance in data collection. cyl and whw prepared and revised the manuscript. anu and cyl helped to analyze the data. yhc ,spt and pll revised and edited the manuscript. mly and swf conceived the study and revised the draft. key: cord-305763-160heazx authors: lai, chih-cheng; wang, jui-hsiang; hsueh, po-ren title: population-based seroprevalence surveys of anti-sars-cov-2 antibody: an up-to-date review date: 2020-10-09 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.011 sha: doc_id: 305763 cord_uid: 160heazx severe acute respiratory syndrome coronavirus 2 (sars-cov-2), causing the coronavirus disease 2019 (covid-19), has led to a global pandemic. however, the majority of currently available data are restricted to laboratory-confirmed cases for symptomatic patients, and the sars-cov-2 infection can manifest as an asymptomatic or mild disease; therefore, the true extent of the burden of covid-19 can be underestimated. improved serological detection of specific antibodies against sars-cov-2 can help estimate the true number of infections. this article comprehensively reviewed the associated literature and provides updated information regarding the seroprevalence of the anti-sars-cov-2 antibody. the seroprevalence can vary according to different sites and the seroprevalence can increase with time in the longitudinal follow-up. although healthcare workers (hcws), especially those caring for covid-19 patients, are considered as a high-risk group, the seroprevalence of a hcw wearing adequate personal protective equipment is thought to not be higher than other groups. with regard to sex, no statistical difference has been found between male and female subjects. some, but not all, studies have shown that children have a lower risk than other age groups. finally, seroprevalence can vary according to different populations, such as pregnant women and hemodialysis patients; however, limited studies have examined these associations. furthermore, continued seroprevalence surveillance is warranted to estimate and monitor the growing burden of covid-19. mild infections, and in places where qrt-pcr is unavailable. these issues can limit the understanding of the extent of sars-cov-2 infections and further affect the implementation of infection control and prevention policy. to solve this issue, the use of a serologic test to detect anti-sars-cov-2 antibody can be a better way to estimate the burden of sars-cov-2 infection than the pcr method, and help to understand the associated epidemiology (lai et al., 2020c; eckerle et al., 2020; ko et al., 2020; . therefore, we conducted this review to provide updated and comprehensive information about the seroprevalence of the sars-cov-2 antibody in different populations. several large population-based studies (pollán et al., 2020; stringhini et al., 2020; fiore et al., 2020; vena et al., 2020; gallian et al., 2020; bogogiannidou et al., 2020; silveira et al., 2020; amorim et al., 2020; sood et al., 2020; ng et al., 2020; rosenberg et al., 2020; havers et al., 2020; nir et al., 2020; sutton et al., 2020; mclaughlin et al., april 27, 2020 to may 11, 2020 households were initially selected from municipal rolls, using a two-stage random sampling stratified by province and municipality size. a total of 61,075 participants received the point-of-care test (orient gene biotech covid-19 igg/igm rapid test cassette; zhejiang orient gene biotech, zhejiang, china; reference gccov-402a), and among them, 51,958 further received a chemiluminescent microparticle immunoassay for the qualitative detection of igg against sars-cov-2 nucleoprotein (sars-cov-2 igg for use with architect; abbott laboratories, abbott park, il, usa; reference 06r8620). the seroprevalence was found to be 5.0% (95% ci, ) by the point-of-care test and 4.6% (95% ci, 4.3-5.0) by immunoassay, with a specificity-sensitivity range of 3.7% (95% ci, 3.3-4.0; both tests positive) to 6.2% (95% ci, 5.8-6.6; either test positive) (pollán et al., 2020) . a study in switzerland reported the preliminary results of the surveillance of 2,766 participants from 1,339 households, with a demographic distribution similar to that of the canton of geneva between april 6 and may 9, 2020 (stringhini et al., 2020) . in this study, 12 weekly seroprevalence surveys, using a commercially available enzyme-linked immunosorbent assay (elisa) (euroimmun; lübeck, germany #ei 2606-9601 g) targeting the s1 domain of the spike protein of sars-cov-2 (sera diluted 1:101), were processed on a eurolabworkstation elisa (euroimmun) (serocov-pop study). the results estimated the seroprevalence to be j o u r n a l p r e -p r o o f 7 4.8% (95% ci, 2.4-8.0; n = 341) in the first week, 8.5% (95% ci, n = 469) in the second week, 10.9% (95% ci, 7.9-14.4; n = 577) in the third week, 6.6% (95% ci, 4.3-9.4; n = 604) in the fourth week, and 10.8% (95% ci, 8.2-13.9; n = 775) in the fifth week (stringhini et al., 2020) . in denmark, a total of 20,640 blood donations were given by 17-69-year-old donors from april 6 to may 3, 2020, which were then subjected to a plasma or whole blood lateral flow test according to the manufacturer's recommendations (igm/igg antibody to sars-cov-2 lateral flow test; livzon diagnostics inc., zhuhai, guangdong, china) (erikstrup et al et al., 2020) . the overall unadjusted seroprevalence was 2.0% (95% ci, 1.8-2.2), and after adjusting for assay sensitivity and specificity (including their ci), the overall seroprevalence was 1.9% (95% ci, 0.8-2.3) (erikstrup et al et al., 2020) . in italy, 390 blood donors in the lodi red zone were recruited, from march 18 to april 6, 2020, for a study that utilized the sars-cov-2 microneutralization assay (percivalle et al., 2020) . a total of 91 (23%) participants were positive for sars-cov-2 specific neutralizing antibodies (≥ 1:10), while 299 (77%) tested negative (< 1:10). contrastingly, the seroprevalence was only 0.99% (n = 9) among 904 healthy blood donors in the apulia region, south-eastern italy (fiore et al., 2020) . recently, one large series including 3609 adult volunteer s from five administrative departments of the liguria and lombardia regions showed the seroprevalence was 11.0% (n = 389 ) (vena et al., 2020) . in france, 998 samples j o u r n a l p r e -p r o o f collected from blood donors during the last week of march or the first week of april 2020 were tested for neutralizing antibodies against sars-cov-2, and the overall seroprevalence was found to be low (2.7%, n = 27) (gallian et al., 2020) . by contrast, one more updated surveillance conducted between may 4 and june 23, 2020 in france showed the higher adjusted estimates of seroprevalence (positive anti-sars-cov-2 elisa igg result against the spike protein of sars-cov-2) were 10.0% (95% ci, 9.1-10.9) and 9.0% (95% ci, 7.7-10.2) in the ile-de-france or grand est, respectivelytwo regions with high rates of covid-19 and 3.1% (95% ci, 2.4-3.7) in the nouvelle-aquitainethe region with a low rate of covid-19 (carrat et al., 2020) . moreover, they noted that confinement is associated with a higher seroprevalence, but a lower seroprevalence was observed in smokers compared to non-smokers (carrat et al., 2020) . during the early stage in greece, the positive rate of anti-sars-cov-2 igg was only 0.36% (24) among 6,586 serum samples, and the crude prevalence was 0.24% (5/2075) and 0.42% (19/4,511) in march and april, respectively (bogogiannidou et al., 2020) . in brazil, three rounds of probability sample household surveys in the state of rio grande do sul were carried out in nine large municipalities using the wondfo lateral flow point-of-care test for igm and igg against sars-cov-2 (https://en.wondfo.com.cn/product/wondfo-sars-cov-2-antibody-test-lateral-flowmethod-2/). the seroprevalence was estimated to be 0.048% (2/4,151; 95% ci = 0.006-j o u r n a l p r e -p r o o f 9 0.174) on 11-13 april, 2020 (round 1), 0.135% (6/4,460; 95% ci = 0.049-0.293) on 25-27 april, 2020 (round 2), and 0.222% (10/4,500; 95% ci = 0.107-0.408) on 9-11 may, 2020 (round 3) (silveira et al., 2020) . furthermore, a significant upward trend was observed throughout the surveys (silveira et al., 2020 (sood et al., 2020) . in san francisco bay area, the seroprevalence was tested using the architect sars166 cov-2 anti-nucleocapsid protein igg and was found to be only 0.1% in 1,000 blood donors in march 2020 (ng et al., 2020 j o u r n a l p r e -p r o o f 2020) (havers et al., 2020) . in indiana, the seroprevalence among 3,658 randomly selected noninstitutional participants was 1.01% (n = 38) between april 25 and 29, 2020 (nir et al., 2020) . in oregon, the overall seropositivity was 1.0% (n = 9) among 897 participants from 19 facilities participating in the influenza-like illness surveillance network (sutton et al., 2020) . in blaine county, 208 out of 917 adult residents had positive anti-sars-cov-2 igg and the overall seroprevalence was 22.7% between may 4 and 9 (mclaughlin et al., 2020). the highest seroprevalence was found to be 31.5% among 200 asymptomatic residents in chelsea, massachusetts (naranbhai et al., 2020) . in china, a serological survey was conducted in seven cities, including hubei province (wuhan, honghu, and jingzhou), guangdong province (guangzhou and foshan), sichuan province (chengdu), and chongqing between march 9, 2020 and april 10, 2020, and a validated serological test for the presence of antibodies (igm or igg) against sars-cov-2 was tested in a total of 17,368 individuals. for 10,499 individuals in the community setting, the seropositivity ranged from 0.6% among 9,442 community residents in chengdu, sichuan, and 1.4% among factory workers in guangzhou, guangdong, to 3.2% among 219 hcws relatives, and 3.8% among 346 hotel staff members in wuhan, hubei . moreover, seropositivity progressively decreased in other cities as the distance to the epicenter j o u r n a l p r e -p r o o f increased . in pakistan, 24 (15.6%) of 154 asymptomatic young policemen had positive anti-sars-cov-2 igg in high-risk areas of lahore (chughtai et al., 2020) and 21.4% to 37.7% of 380 healthy blood donor in karachi (younas et al., 2020) . in malaysia, the seropositivity of anti-sars-cov-2 igg was 0.6% (2/327) and 0.4% (1/261) based on the collected serum samples for non-respiratory-respiratory infections during the pandemic and post-pandemic period, respectively . in seoul, korea, the seroprevalence was only 0.07% based on the surveillance of 1500 residual sample from outpatients of two university hospital (noh et al., 2020) . in summary, the seroprevalence ranges from < 0.1% to more than 20% in the different regions and can increase with time (table 1) . regular monitoring of the seroprevalence in each site should be indicated to establish the epidemiology of covid-19. nosocomial transmission of sars-cov-2 is common within hospitals and covid-19 is a threat for hcws, especially those without appropriate personal protective equipment (ppe) (houlihan et al., 2020; hunter et al., 2020; kluytmans et al., 2020; lai et al., 2020; keeley et al., 2020; wei et al., 2020) . one population-based study demonstrated that the positive rate of anti-sars-cov-2 igg or igm in the j o u r n a l p r e -p r o o f hospital settings was 2.5% (170/6919), which was higher than that reported in the community setting (0.8%, 81/10,449) . in this study , the positive rate was highest for hcws in wuhan, hubei (3.8%, 27/714). many studies had evaluated the seroprevalence among hcws (steensels et al., 2020; martin et al., 2020; korth et al., 2020; stubblefield et al., 2020; pallett et al., 2020; grant et al., 2020; hunter et al., 2020; self et al., 2020; moscola et al., 2020; plebani et al., 2020 hcws who regularly had direct contact with units housing adult covid-19 patients in the month prior to undergoing testing with the validated enzyme-linked immunosorbent assay against the extracellular domain of the sars-cov-2 spike protein (stubblefield et al., 2020) . overall, 19 (7.6%) healthcare personnel tested positive for sars-cov-2 antibodies, and seropositivity was more common among those who were reported to generally not be wearing ppe for all encounters, versus those who were reported to be always wearing ppe (15.8% versus 4.3%) (p = 0.07) (stubblefield et al., 2020) . in china, 105 hcws exposed to four laboratory-confirmed covid-19 patients received testing with an enzyme immunoassay (eia), as well as a microneutralization assay to assess the seroprevalence on day 14 th of quarantine, in which, 17.14% (n = 18) of hcws were seropositive . a higher risk of seroconversion was found for . based on the above findings (table 2) , hcws are at high risk of acquiring sars-cov-2 infection, and adequate ppe could help protect them from the covid-19 infection. in the uk, a multicenter investigation showed that the seroprevalence was 10.6% and 44.7% among 405 asymptomatic and 1,299 symptomatic hcws (pallett et al., 2020) . in another investigation in the uk, an overall seropositivity rate of 31.6% among hcw was found, which was highest among staff working in a clinical environment with direct patient contact (34.7%) and lowest among those working in nonclinical environments without patient contact (22.6%) (grant et al., 2020) . in contrast, one study in the us showed that employees with heavy covid-19 exposure had antibody prevalence similar to those with limited or no exposure and suggested that ppe use seems effective in the prevention of covid-19 infection in healthcare workers (hunter et al., 2020) . another study showed the similar findings that seroprevalence was lower among personnel who reported always wearing a face covering while caring for patients (6%), compared with those who did not (9%) (self et al., 2020) . in the largest cohorts enrolling 40,329 hcws at new york city, the overall seroprevalence was 13.7% (n = 5,523); however, only 9.0% (n = 3,077) among 34,251 without pcr testing were several population-based studies (pollán et al., 2020; 13 stringhini et al., 2020; , amorim et al., 2020; sood et al., 2020; rosenberg et al., 2020) have demonstrated differences in seroprevalence rates among male and female subjects. in new york, the weighted seroprevalence rate of males was 14.8% (95% ci, 13.8-15.8), which was numerically higher than that of females (13.3%; 95% ci, 12.4-14.2) ( rosenberg et al., 2020) . in switzerland, the rate of positive sars-cov-2 serology tests among males was 9.0% (118/1312), which was higher than that among females, at 6.9% (101/1454) (erikstrup et al., 2020) . in los angeles, the unweighted portion of the population positive for igm or igg among males was 5.18% (95% ci, 3.10-8.07), which was numerically higher than that among females (3.31%; 95% ci, 1.94-5.24) (sood et al., 2020) . in brazil, males had a higher seroprevalence, after adjustment, than females (4.1% vs 3.5%, respectively), but the difference was not statistically significant (or, (pollán et al., 2020) . in the us, there was no clear association between seroprevalence by sex across sites (havers et al., 2020) . overall, these findings indicated that the seroprevalence between males and females is not significantly different. three population-based studies (pollán et al., 2020; stringhini et al., 2020; havers et al., 2020; sutton et al., 2020 ) demonstrated a lower seroprevalence among children. compared to subjects aged 20-49 years, children aged 5-9 years had a significantly lower seroprevalence of 0.8% (1/123) (relative risk, 0.32; 95% ci, 0.13-0.63) in a swiss surveillance study (serocov-pop) (stringhini et al., 2020) . in spain, the ene-covid study showed that the seroprevalence of subjects aged 0-19 years was 3.4% using the point-of-care test, and 3.8% by immunoassay, which were lower than those reported for any other age group (4.4-6.0% using the point-of-care test, and 4.5-5.0% by immunoassay) (pollán et al., 2020) . in the united states, the seroprevalence of subjects aged 0-18 years ranged from 0.7% (95% ci, 0-2.5) in western washington state to 5.8% (95% ci, 0-14.3) in minneapolis-st paul-st cloud metro area (minnesota) (havers et al., 2020) . moreover, the seroprevalence of this age group was numerically lower than that of other age groups in western washington state, new york, louisiana, missouri, and connecticut (havers et al., 2020) . in addition, a cross-section study using the novel coronavirus (2019-ncov) igg/igm test kit (colloidal gold; genrui biotech inc, china) was conducted 8-10 weeks after a school outbreak, and the results showed antibody positivity rates of 9.9% (95% ci: 8.2-11.8) for 1,009 students (table 2) . moreover, the positivity was associated with a younger age (p = 0.01), lower grade (p = 0.05), prior rt-pcr positivity (p = 0.03), and history of contact with a confirmed case (p < 0.001) (torres et al., 2020) . in another study (dingens et al., 2020) , the seroprevalence in children who had visited seattle children's hospital during the initial seattle outbreak was determined using abbott sars-cov-2 igg chemiluminescent microparticle immunoassay, and only 8 children were found to be seropositive, with a seroprevalence of 0.7% (table 2) . overall, children seem to have a lower seroprevalence than adults, which was consistent with previous epidemiological findings of laboratory-confirmed covid-19 cases wang et al., 2020; huang et al., 2020; . pregnant women can be infected by sars-co-2, although data in this population are limited (ashraf et al., 2020; barbero et al., 2020; sahin et al., 2020; j o u r n a l p r e -p r o o f 2020; schmid et al., 2020; yu et al., 2020) . recently, 1,293 parturient women were tested using an elisa for sars-cov-2 igg and igm antibodies to the spike receptorbinding domain antigen at two centers in philadelphia from april 4 to june 3, 2020. the results demonstrated that 80/1,293 (6.2%) of parturient women possessed igg and/or igm sars-cov-2-specific antibodies ( (gallian et al., 2020) . patients undergoing hemodialysis are also at risk for covid-19 transmission due to the need for frequent hospital stays, and therefore, the difficulty in maintaining physical distancing (yau et al., 2020; tang et al., 2020; arslan et al., 2020) . the j o u r n a l p r e -p r o o f seroprevalence of hemodialysis patients ranged from 2.8% (16/563) to 3.6% (35/979) in a study in china (31). another study showed the overall sars-cov-2 seroprevalence was 36.2% (129/356) in hemodialysis patients, and 40.3% (n =52) of them were asymptomatic or with negative pcr results (clarke et al., 2020) . in this review, we found no significant association between the incidence of covid-19 cases and their associated seroprevalence (table 1) . even in the same country, the seroprevalence ranged from 0.1% to 12.5%, and 0.05% to 4.0% in the us and brazil (20, (22) (23) (24) 26) , respectively. these findings may be due to the fact that anti-sars-cov-2 antibody seroprevalence varies according to the different study countries/regions, study populations, timing during the period of the covid-19 pandemic, and methods used for serology tests. therefore, the seroprevalence reported in this article can only reflect the situation of the time and place in which the surveillance investigation was performed by the specific test methods. in fact, the number of covid-19 cases is still rapidly growing, and given the time-sensitivity, a true estimation of the epidemiology of sars infection remains a great challenge. therefore, such seroprevalence surveillance should be continued and is necessary to the seroprevalence can vary across different regions and can increase with time in the longitudinal follow-up. although hcws, especially those caring for covid-19 patients, are considered a high-risk group, their seroprevalence would not be higher than that observed in other groups if they wear adequate ppe. regarding sex, no statistical difference was found between male and female subjects. some studies have shown that children have a lower risk than other age groups, while others did not. finally, the seroprevalence can vary according to different populations, such as in pregnant women and patients undergoing hemodialysis; however, relevant studies are limited. therefore, further continued seroprevalence surveillance is warranted to estimate and monitor the growing burden of covid-19. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. no funding was required. j o u r n a l p r e -p r o o f no ethical approval sought. we declare no conflict of interest. j o u r n a l p r e -p r o o f seroprevalence of anti-sars-cov-2 among blood donors in rio de janeiro incidence and immunologic analysis of coronavirus disease (covid-19) in hemodialysis patients:a single-center experience covid-19): a systematic review of pregnancy and the possibility of vertical transmission sars-cov-2 in 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retrospective, single-centre, descriptive study chelsea biomedomics sars-cov-2 combined igm/igg lfa key: cord-330819-vfagxsdz authors: althouse, benjamin m; flasche, stefan; minh, le nhat; thiem, vu dinh; hashizume, masahiro; ariyoshi, koya; anh, dang duc; rodgers, gail l.; klugman, keith p.; hu, hao; yoshida, lay-myint title: seasonality of respiratory viruses causing hospitalizations for acute respiratory infections in children in nha trang, vietnam date: 2018-08-14 journal: int j infect dis doi: 10.1016/j.ijid.2018.08.001 sha: doc_id: 330819 cord_uid: vfagxsdz background: acute respiratory infections (aris) are the most common causes of death in children under 5 years of age. while the etiology of most pneumonia and ari episodes is undiagnosed, a broad range of ari-causing viruses circulate widely in south east asia. however, the patterns and drivers of the seasonal transmission dynamics are largely unknown. here we identify the seasonal patterns of multiple circulating viruses associated with hospitalizations for aris in nha trang, vietnam. methods: hospital based enhanced surveillance of childhood ari is ongoing at khanh hoa general hospital in nha trang. rt-pcr was performed to detect 13 respiratory viruses in nasopharyngeal samples from enrolled patients. seasonal patterns of childhood ari hospital admissions of various viruses were assessed, as well as their association with rainfall, temperature, and dew point. results: respiratory syncytial virus peaks in the late summer months, and influenza a in april to june. we find significant associations between detection of human parainfluenza 3 and human rhinovirus with the month's mean dew point. using a cross-wavelet transform we find a significant out-of-phase relationship between human parainfluenza 3 and temperature and dew point. conclusions: our results are important for understanding the temporal risk associated with circulating pathogens in southern central vietnam. specifically, our results can inform timing of routing seasonal influenza vaccination and for when observed respiratory illness is likely viral, leading to judicious use of antibiotics in the region. acute respiratory infections (aris) in south east asia cause substantial morbidity and mortality, especially in children under 5 years of age (walker et al., 2013) . pneumonia continues to be the number one cause of under 5 death despite effective treatments (wardlaw et al., 2006) . a substantial contributor to this is the largely unknown etiology of most pneumoniae, with both viral and bacterial origin. the patterns of pneumonia and other ari hospitalizations serves as a proxy for determining the transmission dynamics of viruses and bacteria contributing to these hospitalizations, and is of key importance in understanding and limiting burden of this childhood killer. in addition to informing on the relative likelihood of the potential viral etiology of a pneumonia case based on seasonally circulating pathogens, knowledge of seasonal influenza epidemiological dynamics can aid in informing optimal timing for vaccination efforts (saha et al., 2014; lambach et al., 2015) and judicious use of antivirals tanaka et al., 2014) . identification of low incidence seasons would provide a target window for vaccination, with the hope of maximizing population immunity before the onset of the influenza season. similarly, when respiratory syncytial virus (rsv) vaccination becomes available, knowledge of its seasonality will be useful to maximize benefit (drysdale et al., 2016; anderson et al., 2013) , and in the potential administration of passive immunoprophylaxis with palivizumab to reduce the number of severe outcomes associated with rsv infection among high-risk infants (committee on infectious diseases, 2009 ). finally, knowledge of seasonal patterns of virus circulation can inform the clinical use of antibiotics, again limiting use when viral circulation is traditionally high to minimize antibiotic resistance ( van nguyen et al., 2013; laxminarayan et al., 2013 laxminarayan et al., , 2016 van boeckel et al., 2014) . previous work has identified the potential etiology of pneumonia and other aris in southern central vietnam (do et al., 2011; yoshida et al., 2010) . adenovirus (aov), bocavirus (hbov), coronavirus (cov), human metapneumovirus (hmpv), human parainfluenza 1-4 viruses (hpiv1-4), human rhinovirus (hrv), influenza a and b, and rsv all contribute to the disease burden and circulate widely. information on viral transmission dynamics across seasons in vietnam is relatively under-explored. do et al. found seasonality of rsv infections and slight seasonality of hmpv infections in ho chi minh city, but no seasonality of influenza (do et al., 2011) . several studies have similarly found high variability in influenza a & b incidence over the year (nguyen et al., 2007; le et al., 2015; thai et al., 2015) . yoshida et al. found rsv occurring in the hot months, influenza a in the cool months, and year-round detection of hrv in nha trang (yoshida et al., 2010) . few other studies have examined seasonality of these common viruses across south east asia. here we examine the seasonal trends of hospitalizations and circulation of multiple viruses in nha trang, vietnam. using enhanced hospital based surveillance of childhood ari we identify seasonal patterns in hospitalizations as a proxy for transmission and explore the relationship of hospitalizations associated with virus detection with rainfall, temperature, and dew point, to try and identify contributing factors to observed seasonality. the study site is nha trang, central vietnam, where the study population has been described previously (yoshida et al., 2014 (yoshida et al., , 2010 flasche et al., 2014) . the hospital based enhanced surveillance of childhood ari is ongoing. we analyze data from january 29, 2007 to april 26, 2012 which is the only tertiary care facility located in khanh hoa province. according to the field site census survey in july 2006, the study catchment area encompassing the 16 non-touristic of the 27 communes in nha trang city, had 198,729 residents including 13,952 children less than 5 years of age. an ari case was defined as any child presenting to khgh with cough or/and difficulty in breathing. before study enrollment, informed consent was obtained from parents of children who presented with ari and lived in the study catchment area. clinical and demographic information, chest radiographs (cxr), laboratory data, and nasopharyngeal (np) samples were collected from all enrolled patients. khgh is the only hospital in nha trang, khanh hoa province and the only one accessible for residents of the catchment area. hence for incidence calculations we assume that all children with ari are eligible to be hospitalized and enrolled into the study and use the population of the catchment area as denominator. acute respiratory infection patients with normal cxr were categorized as upper respiratory tract infection (urti). patients with abnormal cxr were categorized as lower respiratory tract infection (lrti). np samples were collected at the time of admission and viral nucleic acid was extracted using qia viral rna minikit (qiagen inc., valencia, ca). four multiplex-pcr assays (1: influenza a, influenza b, rsv, hmpv; 2: piv-1, -2, -3, and -4; 3: rhinovirus, coronavirus 229e, coronavirus oc43; 4: adenovirus and bocavirus) were performed to detect 13 respiratory viruses in each np sample. a second confirmatory-pcr was performed for samples positive on the initial pcr test. samples positive for both pcr assays were defined as positive. reverse transcription-pcr (rt-pcr) assays were performed using one-step rt-pcr kit from qiagen. for the multiplex pcr and hemi-nested pcr assays, taqdna polymerase (promega, san luis obispo, ca) was used as previously described (yoshida et al., 2010) . positive templates were used in each assay for quality control. three weather variablesrainfall (inches), temperature (f ), and dew point (the temperature to which air must be cooled in order to reach saturation with water)were collected from the nha trang station (id: 488770) reported by the us national oceanic and atmospheric administration (national oceanic and atmospheric administration, 2017). we considered monthly averages of all weather variables as well as both the weather variable on the day of admission (t 0 ) as well as averaged over the previous 7 days (t à7 to t à1 ) assuming up to a week incubation period for the viral infections (see supplementary material) (lessler et al., 2009) . the weather in nha trang central vietnam is warm throughout the year (between 20 and 30 c ). in terms of temperature, december to february months are cooler (referred to here as the winter months) while june to august months are hottest months (referred to here as the summer months). september, october, november are the wettest months. for each pcr+ for virus a series of log-link poisson models were fit to assess respective seasonality with calendar month as the main predictor, log-commune population size as an offset term, monthly averaged rainfall, temperature, and dew point, and calendar year as adjusting variables. the outcome was monthly aggregate cases, with resulting coefficients as incidence rate ratios as compared to january. we excluded hospitalizations with more than one virus detected in the nasopharynx to adjust for a potential bias through inclusion of cases who by virtue of being co-infected may otherwise have been asymptomatic (althouse and scarpino, 2015) . this approach underestimates the true incidence of np carriage among ari cases but allows estimation of seasonal patterns that are not biased by other circulating viruses; although co-circulation of bacteria was not accounted for. we assessed the numbers and variety of viruses in ari hospitalizations using binomial proportion tests for each virus. to examine the relationship between monthly average rain, temperature, and dew point and incidence hospitalized childhood ari infections, we estimated the cross-wavelet transform between the z-standardized time series (we subtracted the mean of the time series and divided by the standard deviation) of weather and viral detections (cazelles et al., 2008) . the cross-wavelet transform identifies regions of high power in phase-space and identifies the relative phases of each time series, i.e., in-phase or out-of-phase (grinsted et al., 2004) . the wavelet transform can be thought of a fourier transformation over time that can identify what is the dominant frequency composing a time series as the signal changes in time. the cross-wavelet transform allows us to compare how two time signals co-vary: we can identify if the presence of a particular frequency at a given time in the time series of hospitalizations corresponds to the presence of that same frequency at the same time in a weather covariate (chaves and pascual, 2006) . additionally, we can identify the magnitude by which weather precedes or follows hospitalizations through the phase angle of the two time series. finally, we can identify the statistical significance of the identified constituent frequencies over time by comparing the observed frequencies to a red-noise process. sensitivity analyses, presented in the supplementary materials, were performed as follows: 1) case counts of less than 70 per virus over the whole study period were deemed too low for robust statistical inference; 2) alternative poisson regression models where the reference category is july; 3) logistic regression models were formulated as an alternative to the poisson regressions above with detection of a virus by pcr (yes/no) as the outcome, with month as the main predictor, adjusted for weather, commune of residence, age, sex, smoking indoors, socioeconomic status (ses), and calendar year, with weather variables on the day of admission (t 0 ) as well as averaged over the previous 7 days (t à7 to t à1 ); and 4) additional wavelet analyses of viral isolations not presented in the main text. the study enrolled 3431 children between 2007 to 2013. among those, 374 (11%) had multiple viruses detected in their np swabs, for 59 presence of viruses in the np was not determined, and were excluded from the analyses, thus the total study population was 2998. among all cases with a virus detected, hrv, rsv, and influenza a were the most frequently detected viruses, with 569 (33.5% of all viral detections), 455 (26.8%), and 282 (16.6%) detections, respectively (table 1 and figure 1 ). counts of bocavirus (hbov), coronavirus (cov), and human parainfluenza 1, 2, and 4 viruses (hpiv1-4) were less than 70 and are reported in the supplementary material. strong seasonality, as defined by at least three consecutive months with a consistently higher or lower incidence than expected (irr or or greater or less than 1, respectively) and at least one of those statistically significantly different from the baseline, was observed for influenza a, rsv, and the presence of any virus (figures 2 and 3) . rsv peaked in july through november, with august seeing a 15.69 (95% confidence interval [ci]: 3.05, 80.56) times higher risk of identifying rsv as the sole viral agent from the nasopharynx of a childhood case as compared to january. influenza a peaked in may with an irr of 6.28 (95% ci: 2.2, 17.89) as compared to january. estimates of odds ratios from the supplemental logistic regression are qualitatively similar to the poisson regression, save for hpiv3, which exhibits a consistent yet nonsignificant peak in the cool months in the primary analysis which becomes significant in the supplemental analysis (see supplemental material). weather patterns over the study period were similar to patterns before and after the study period (supplementary material, figure s3 ). monthly average rainfall (in inches), temperature (1 f), and dew point (1 f) correlated with the seasonality of some of our endpoints. figure 4 shows the incidence rate ratios for the three weather effects from the seasonally-adjusted models. overall hospitalizations for ari were negatively associated with temperature (irr 0.92 per 1 degree increase, 95% ci: 0.87, 0.97, p = 0.003) and positively associated with dew point (irr 1.08 per 1 degree increase, 95% ci: 1.04, 1.13, p < 0.001). of the few other significant effects, influenza a and hrv had a negative associations with temperature (irr 0.85, 95% ci: 0.75, 0.9, p = 0.0116, and irr 0.86, 95% ci: 0.79, 0.94, p < 0.001, respectively), and hpiv3 and hrv were positively associated with dew point, with irrs 1.26 (95% ci: 1.04, 1.52, p = 0.0164) and 1.13 (95% ci: 1.05, 1.21, p = 0.0009), respectively. logistic regression found that rsv was positively associated with the previous week's rain, with an odds ratio of of 1.90 (95% ci: 1.21, 2.99, p = 0.0053). previous week's temperature was marginally associated with rsv (or: 1.14 (95% ci: 0.98, 1.33, p = 0.08) (see supplementary material). figure 5 shows the cross-wavelet transform of all hospitalizations and the three weather variables in the month of admission. significant bands of high power around 1 year can be seen for temperature and dew point. this indicates that hospitalizations and temperature and dew point share variability at yearly frequencies over the study period, and the phase relationship indicates that changes in weather slightly precede changes in hospitalizations (arrows point about 45 down). figure 6 shows the cross-wavelet transform of rsv and the three weather variables with similar significance bands around 1 year for temperature and dew point. the phase indicates temperature and dew point lead rsv incidence. while not significant, rsv was found to be leading rainfall by 90 (3 months) at the one year period band (see supplementary material). significant bands of power were seen between temperature and dew point with hpiv3 with an indicated phase relationship of nearly completely out-of-phase (figure 7) . similar patterns were seen (1 year significant bands between temperature and dew point and virus) for adv, hbov, cov, hpiv1,2&4, hrv, and influenza a, though the phase differences varied across these viruses; hmpv and influenza b had bands lying outside the cone of influence (ie, not statistically significant; see supplementary material). these results in general indicate strong associations between weather covariates and viral hospitalizations at a yearly timescale. here we have identified seasonal trends of several common respiratory viruses in hospitalized children in nha trang, vietnam. by fitting a series of statistical models to the observed data, we allow the data to identify salient features contributing to the seasonality of these viruses. we evaluated seasonal patterns and associations with weather of hospitalizations for several respiratory viruses using three lines of evidence: 1) poisson regression examining the relative incidence across months of virus detections adjusted for weather covariates, 2) cross-wavelet transforms of hospitalizations with viral detections, and 3) a sensitivity analysis with a logistic regression model finding odds ratio of hospitalizations with viral detections and weather variables. any viral detection showed distinct seasonality with peaks in may through september, a negative association with temperature, positive association with dew point, and crosswavelets indicating temperature and dew point leading viral detection. of commonly detected viruses, rsv, influenza a, and hpiv3 had significant seasonality. rsv peaked in july through december, was positively associated with the week's previous average rainfall. cross-wavelets showed temperature and dew point to lead rsv, rain was found to non-significantly fall behind rsv at 1 year frequencies, and precede rsv at shorter (<100 day) frequencies. finally, hpiv3 while not significant, had peaks in january and february, was positively associated with dew point, and was completely out of phase with temperature and dew points in cross-wavelet analyses. these results contribute to the growing body of knowledge on the epidemiology of respiratory pathogens in south east asia and southern central vietnam. using a cross-wavelet transform we evaluated the timedependence of virus hospitalizations with the weather covariates. we found strong yearly associations with rsv over the study period with temperature and dew point in phase with hospitalizations. this seasonality is opposite to observed seasonality in temperate climates, where rsv typically peaks in winter (tang and loh, 2014; shek and lee, 2003) . recent reviews of rsv seasonality in tropical regions highlights the uncertainty in the effects of weather on rsv transmission. studies in brazil (straliotto et al., 2002) , hawaii (reese and marchette, 1991) , india (agrawal et al., 2009) , kenya (hazlett et al., 1988) , and malaysia (chew et al., 1998; chan et al., 2002; khor et al., 2012) , have shown negative associations between temperature and rsv, while studies in hong kong (chan et al., 1999) , mexico (yusuf et al., 2007) , singapore (chew et al., 1998) , and taiwan (huang et al., 2001) have shown positive associations. we find strongly positive associations between temperature and rsv hospitalizations with a slight lead of temperature on rsv. this is evident both from the cross-wavelet transform and the regression results indicating a positive effect of the previous week's temperature on rsv. there is less uncertainty in the role of rainfall on rsv transmission in tropical areas, where the majority of work indicates that rsv generally occurs during rainy seasons (shek and lee, 2003) . colombia (bedoya et al., 1996) , the gambia (weber et al., 1998) , hong kong (chan et al., 1999) , kenya (hazlett et al., 1988) , malaysia (chan et al., 2002) , and papua new guinea (hierholzer et al., 1994) all show positive rsv associations with rainfall. omer et al. (omer et al., 2008) showed significant positive associations between rainfall and temperature in the previous 8 days and rsv incidence in lombok, indonesia. we find similar associations, with the mean rainfall and temperature over the previous 7 days having odds ratios for rsv of 1.90 and 1.14, respectively. this association is plausible as the incubation period of rsv is estimated to be between 4 and 5 days (lessler et al., 2009) . detailed contact tracing studies, coupled with climatological data could refine this association. somewhat surprisingly, the cross-wavelet transform of rsv and rain showed no significant association, though areas of high power were observed in the 1-year and 6-month bands, with phase indicating rsv leading weather. however, none of the viruses studied here showed appreciable associations with rain in the cross-wavelet transform, possibly indicating the dominance of other weather effects (temperature and dew point) on virus hospitalizations. as with previous studies examining hpiv incidence, we found a predominance of hpiv3 (72 detections) compared to 41, 13, and 3 for hpiv1, 2, and 4, respectively. typical seasonality for hpiv3 is the spring and early summer months in the temperate regions (fry et al., 2006; hall, 2001) , and has little to no observed seasonality in the tropics and subtropics (chew et al., 1998; branche and falsey, 2016) . we find evidence for winter peaks in hpiv3 hospitalizations when employing both the poisson regression model as well as the logistic regression model to estimate odds ratios, though the peaks were not statistically significant when controlling for weather. the cross-wavelet transforms reveals hpiv3 to vary significantly at 1 year periodicity with temperature and dew point across the study. it also shows that hpiv3 hospitalizations are nearly completely out of phase with temperature and dew point throughout the study period. hpiv3 has been associated with low temperature and low relative humidity (miller and artenstein, 1967) though there is in general a paucity of data on the transmission routes of hpiv3 (pica and bouvier, 2012; meissner et al., 1984) . future work could explore in more depth the epidemiological relationship between hpiv and weather variables. this study is not without limitations. first, while we have nearly 6 years of data, this is still a relatively short period to assess longterm seasonal trends, or to increase confidence in the estimates of seasonal patterns. however, the length of the analyzed time series is similar to other studies examining seasonal trends in viral respiratory pathogens in the tropics (chew et al., 1998; hall, 2001) , and gives indications for areas of future study. second, we excluded individuals with more than one virus detected. examination of changes in the seasonality of other viruses and coinfection over this period is worthy of study and is outside the scope of this paper. third, this study used hospital-based surveillance, necessarily presenting the most ill children. we take as an assumption that hospitalizations are a fraction of all transmission and severity of illness is not related to weather. finally, this study examines the influence of weather on viral hospitalizations and does not address other drivers of seasonal patterns of transmission, such as school closures (fine and clarkson, 1982) , differences in other social behavior such as contact rates (cook et al., 1990; dushoff et al., 2004) , susceptible recruitment through births (metcalf et al., 2012) , or possible seasonal changes in host immune responses (dowell et al., 2003) . future work examining these drivers in this setting is necessary. limitations aside, our study adds to the body of literature on seasonality of common respiratory patterns in tropical regions and will be of use when consideration of the epidemiology of these pathogens is necessary. for example the timing of influenza peaks in the mid-spring months (april, may, june) would indicate routine vaccination in the winter months would be of biggest impact. similarly, knowing rsv peaks in the late summer/early fall when rcp is at its lowest may help in limiting unnecessary antibiotic (laxminarayan and malani, 2007) or antiviral use (tanaka et al., 2014) . in vietnam and most of asia, most antibiotics are acquired from a pharmacist without a formal prescription ( van nguyen et al., 2013) . this fact makes results like those presented here of high importance to public health decision-makers to inform pharmacists of seasonality of respiratory infection etiologies and urge judicious prescribing practices. additional future work could include examination of the effects of contact clustering (hébert-dufresne and , coinfection hébert-dufresne et al., 2013) , and asymptomatic carriers (althouse and scarpino, 2015) on transmission of the examined viruses all of which may be influenced by weather. comparative evaluation of real-time pcr and conventional rt-pcr during a 2 year 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contributed intellectually: all authors the study was approved by institutional review boards in the national institute of hygiene and epidemiology, vietnam and the institute of tropical medicine, nagasaki university, japan. bma and hh were supported by bill & melinda gates through the global good fund. sf and lmy were partially supported by bill & melinda gates foundation (bmgf opp1139859). the pediatric ari surveillance study in nha trang, vietnam was supported by the japan initiative for global research network on infectious diseases (j-grid) from ministry of education, culture, sport, science & technology in japan, and japan agency for medical research and development (amed). the funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. supplementary data associated with this article can be found, in the online version, at https://doi.org/10.1016/j.ijid.2018.08.001. key: cord-346461-eqyte6ko authors: scialpi, michele title: pneumonia misinterpretation in covid-19: revisitation and update date: 2020-08-28 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.067 sha: doc_id: 346461 cord_uid: eqyte6ko nan and the signs of dad and no signs of suppurative bronchopneumonia are reported histologically. in patients who died from covid-19, autopsy studies revealed pneumonia from 0 to 48% of cases (17) (18) (19) . finally, the histopathological findings in the lung of patients who died of covid-19 are similar to those described in middle east respiratory syndrome coronavirus (mers-cov) (22,23), suggesting similarities in the pathogenesis and the mechanisms of lung tissue damage. in conclusion, the rivisitation of the pneumonia in patients who died of covid-19, revealed a discrepancy between the ct signs identified as "pneumonia, covid-related" and histology. lung histopatologic fetures are mainly related to ada and/or associated with pe and a conseguent respiratory failure causing death in covid-19 patients. these knowledge are essential to improve the clinical approach and to reduce mortality in covid-19 patients. author contributions: study design: ms; writing manuscript: ms; editing manuscript:ms; literature research:ms. the author declares that there are no sponsors for this study. ethical approval not required. the author does not declare any conflict of interest associated for the manuscript entiltled "pneumonia misinterpretation in covid-19: revisitation and update". chest ct for typical 2019-ncov pneumonia: relationship to negative rt-pcr testing clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus-infected pneumonia in wuhan ct imaging features of 2019 novel coronavirus (2019-ncov). radiology. 2020 performance of radiologists in differentiating covid-19 from viral pneumonia on chest ct early clinical and ct manifestations of coronavirus disease 2019 (covid-19) pneumonia ct manifestations of two cases of 2019 novel coronavirus (2019-ncov) 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dysfunction pulmonary vascular endothelialitis, thrombosis, and angiogenesis in covid-19 autopsy findings and venous thromboembolism in patients with covid-19: a prospective cohort study acute pulmonary embolism: relationships between ground-glass opacification at thin-section ct and hemodynamics in pigs pulmonary embolism in patients with covid-19: time to change the paradigm of computed tomography associated with acute respiratory distress syndrome histopathology of middle east respiratory syndrome coronovirus (mers-cov) infection-clinicopathological and ultrastructural study key: cord-284652-7npya3yx authors: shim, eunha; tariq, amna; chowell, gerardo title: spatial variability in reproduction number and doubling time across two waves of the covid-19 pandemic in south korea, february to july 2020 date: 2020-10-08 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.007 sha: doc_id: 284652 cord_uid: 7npya3yx objectives in south korea, 13,745 cases of coronavirus disease (covid-19) have been reported as of 19 july, 2020. to examine the spatiotemporal changes in the transmission potential, we present regional estimates of the doubling time and reproduction number (rt ) of covid-19 in the country. methods daily series of confirmed covid-19 cases in the most affected regions were extracted from publicly available sources. we employed established mathematical and statistical methods to investigate the time-varying reproduction numbers of the covid-19 in korea and its doubling time, respectively. results at the regional level, seoul and gyeonggi province have experienced the first peak of covid-19 in early march, followed by the second wave in early june, withrt exceeding 3.0 and mean doubling time ranging from 3.6 to 10.1 days. as of 19 july, 2020, gyeongbuk province and daegu are yet to experience a second wave of the disease, where the mean rt reached 3.5-4.4 and doubling time ranging from 2.8 to 4.6 days during the first wave. conclusions our findings support the effectiveness of control measures against covid-19 in korea. however, the easing of the restrictions imposed by the government in may 2020 facilitated a second wave in the greater seoul area. since the first covid-19 cases reported in wuhan, hubei province, china, in december 2019, more than 24.7 million cases of coronavirus disease , including more than 830,000 related deaths, have been reported worldwide (who) as of august 30, 2020. in south korea, the novel coronavirus was first diagnosed in a 36-year-old chinese woman who entered the country on 20 january 2020. south korea has since experienced two heterogenous waves of the disease with a total of 13,745 cases including 295 deaths as of 19 july 2020 (kcdc, 2020a) . during the early phase of the covid-19 outbreak in south korea, public health authorities primarily conducted strict contact tracing and isolation of confirmed cases as well as quarantined those suspected with the novel coronavirus (covid-19 national emergency response center et al., 2020) . as the number of covid-19 cases continued to increase, korean public health authorities set the alert to the highest level (level 4) on 23 february and mandated the population to report any symptoms related to for further screening and testing. in addition, the country rapidly adopted a "test, trace, isolate, and treat" strategy that has been deemed effective in stomping out localized outbreaks of the novel coronavirus (kcdc, 2020a) . however, the total number of confirmed cases in south korea spiked from 31 cases on 18 february to 433 on 22 february. according to the korea centers for disease control and prevention (kcdc), this sudden jump was mainly attributed to a super-spreader (the 31 st case) who had participated in a religious gathering of attendees of the shincheonji church of jesus in daegu (kcdc, 2020a) . these superspreading events occurred in the daegu and gyeongbuk provincial regions, leading to more than 5,210 secondary covid-19 cases in korea (kcdc, 2020a , ryall, 2020 . these events facilitated sustained transmission chains, with 38% of the cases in the country associated with the church cluster in daegu (shim et al., 2020b) . on 8 march, the kcdc announced that 79.4% of the total cases had epidemiological links, whereas the remaining 20.6% cases were either sporadic cases or under investigation (kcdc, 2020a) . case clusters started to accumulate from churches in the seoul capital area, and on 17 march, 79 church j o u r n a l p r e -p r o o f attendees developed covid-19 after attending a service at the river of grace community church. notwithstanding social distancing orders put forward by the government, some churches continued to conduct services, which led to new clusters of infections. for instance, the manmin central church in seoul was involved in one of the clusters, with 41 infections linked to a gathering in early march; saengmyeongsu church in gyeonggi province was another church cluster linked to 50 cases (park, 2020) . as sars-cov-2 infection spread rapidly outside korea, the number of imported cases started to increase, resulting in 476 imported (4.9%) cases out of 9,661 total cases as of 30 march. consequently, as of 1 april, the kcdc implemented self-quarantine measures for travellers from europe and the u.s.a (kcdc, 2020a) . in addition, incoming travellers with symptoms but negative test results for coronavirus, as well as asymptomatic short-term visitors were ordered to follow a 2-week quarantine in the government facilities (kcdc, 2020a). such control measures undertaken by south korea have been deemed successful in limiting the spread of the outbreak, without locking down entire cities (normile, 2020) . therefore, after a sustained period of low incidence with fewer than 20 cases per day (16 april -5 may), the government eased its strict nationwide social distancing guidelines on 6 may, with a phased reopening of schools starting mid-may, 2020. however, a new cluster linked to nightclubs in itaewon emerged in central seoul in early may, resulting in a resurgence of cases, that led to a second wave of covid-19 in the greater areas of seoul. as of 29 may, the number of cases that were linked to this cluster had reached 266 (kcdc, 2020a) . accordingly, the seoul city government ordered all clubs, bars, and other nightlife establishments in the city to close indefinitely (kcdc, 2020a). simultaneously, another cluster emerged from an ecommerce warehouse in the gyeonggi province, resulting in 108 cases as of 30 may. in the last week of may, ~40-80 daily new cases of covid-19 were being reported (kcdc, 2020a). following this spike in the number of new covid-19 infections in nearly 2 months, public health authorities reimplemented strict lockdown measures in seoul along with school closure, one more time across the nation. in june, it was announced that the strict social distancing campaign would be j o u r n a l p r e -p r o o f indefinitely extended as a preventive measure in seoul, incheon, and gyeonggi province; however, phased reopening of schools was initiated on may 20. it was reported by the kcdc that a holiday weekend in early may triggered a new wave of infections focused in the greater seoul area, the so-called second wave of covid-19 in south korea (2020) . in seoul, the average number of new daily cases reported from 4 june to 17 june was 43 (kcdc, 2020a). this was followed by sporadic clusters of infections across the country in july, most of them associated with religious facilities and door-to-door salespeople, especially in the densely populated seoul region and adjacent areas. therefore, since 10 july, the government banned churches from organizing small gatherings other than regular worship services (kcdc, 2020a to estimate the regional and temporal variability in the reproduction number of covid-19 in south korea, including the second wave concentrated in the greater seoul areas, we analysed the spatiotemporal progression of the epidemic in the country from mid-february to mid-july 2020. here our focus lies on estimating and interpreting the doubling time and effective reproduction number rt, a metric that quantifies the time-dependent transmission potential of the disease, incorporating the effect of control measures, susceptible depletion, and behavioural changes. this key epidemiological parameter, rt, represents the average number of secondary cases generated per case whenever conditions persist as they were at time t. epidemic doubling times describes the sequence of intervals at which the cumulative incidence doubles (lee et al., 2020 , muniz-rodriguez et al., 2020 . therefore, an increase in the doubling time implies a decline in disease transmission. in this report, we estimated the doubling time and the effective reproduction number involving two epidemic waves of the covid-19 epidemic in south korea by employing the time series of cases by date of symptoms onset for the four most affected korean regions: seoul, gyeonggi province, gyeongbuk province, and daegu. we also discuss the spatiotemporal variability of the reproduction number in terms of the public health policies that were put in place by the korean government. we collected the daily series of confirmed local covid-19 cases in south korea from 20 january to 19 july, which were published by national and local public health authorities, including city or provincial departments of public health in south korea (kcdc, 2020b). we focused our analysis on the regions with the highest caseloads including seoul, gyeonggi province, gyeongbuk province, and daegu ( figure 1 ). for a more accurate estimation of epidemic growth rates, the epidemic curve should be analyzed according to the date of symptom onset rather than the date of reporting because reporting delays can fluctuate substantially over the course of an epidemic. reporting delays distort the incidence pattern of epidemics, misrepresenting the outbreak trajectory, thus possibly affecting the estimation of the reproduction number (tariq et al., 2019) . a prior study suggested that obtaining knowledge about reporting parameters, such as delay patterns and structure improves the estimates of the reproduction numbers (azmon et al., 2014) . however, for the covid-19 data in korea, the date of symptom-onset is only available for 732 cases reported in gyeonggi province, which yielded a mean of 4.5 days and standard deviation of 4.4 days for the distribution of delays from symptoms onset to reporting of cases. therefore, we utilized the empirical distribution of these 732 reporting delays from the onset of symptoms to reporting to impute the missing dates of onset for the remaining cases (shim et al., 2020a) . specifically, we reconstructed 300 epidemic curves according to the date of symptom onset, from which we derived the mean incidence curve of local case incidence (shim et al., 2020a , tariq et al., 2019 . for the calculation of rt(t), the mean incidence curve estimated based on the date of symptom onset was used for the regions of interest (i.e., seoul, gyeonggi province, gyeongbuk province, and daegu) (figure 2 ). using the reconstructed mean incidence curve of local case incidence, we removed the first and last three data points to adjust for the reporting delays in our real-time analysis. we assumed that the first wave ends when the mean incidence becomes less than 0.2 individuals per day. similarly, we assumed that the second wave starts when the mean incidence of local cases becomes greater than 0.5 individuals per day. slight variations to these thresholds did not affect our results. we analyzed the number of times covid-19 cumulative incidence doubled and the evolution of the doubling times in the four most affected areas in korea (i.e., seoul, gyeonggi province, gyeongbuk province, and daegu) from from 20 january to 19 july. using regional-level daily cumulative incidence data, we calculated the times at which cumulative incidence doubles, denoted by . specifically, we assume that where 0 = 0, ( 0 )= 0 ( = 0, 1, 2, 3, … , ), and ( ) denotes the cumulative number of cases at time (muniz-rodriguez et al., 2020) . here, is defined as the total number of times cumulative incidence doubles. specifically, the sequence of doubling times are described as = ∆ = − −1 where = 1, 2, 3, … , . in addition, we used parametric bootstrapping with a poisson error structure around the harmonic mean of doubling times to obtain the 95% confidence interval (chowell et al., 2006a , chowell et al., 2006b . we assume that rt(t) can be estimated by the ratio of the number of new infections generated at time step t (it) to the total infectiousness of infected individuals at time t, given by ∑ − =1 (chong et al., 2018 , fraser, 2007a . here, ws denotes the infectivity profile of the infected individual, which is j o u r n a l p r e -p r o o f dependent on the time since infection (s) but independent of calendar time (t) (he et al., 2020, wallinga and teunis, 2004) . specifically, ws is defined as a probability distribution describing the average infectiousness profile after infection. individual biological factors such as pathogen shedding or symptom severity can affect the distribution ws. the infectivity profile, ws, can be approximated by the distribution of the generation time; however, times of infection are rarely observed, making it difficult to measure the distribution of the generation time (fraser, 2007b) . therefore, the timing of symptoms onset is often used to estimate the distribution of the serial interval (si) instead, which is defined as the time interval between symptom onset in two successive cases in a chain of transmission (cori et al., 2013) . specifically, the infectiousness of a patient is a function of the time since infection and is proportional to ws if we set the timing of infection in the primary case as the time zero of ws and assume that the generation interval equals the si. the si was assumed to follow a gamma distribution with a mean of 4.8 days and a standard deviation of 2.3 days (nishiura et al., 2020) . analytical estimates of rt were obtained within a bayesian framework using epiestim r package in r language version 3.6.3 (r foundation for statistical computing, vienna, austria) (cori et al., 2013) . rt was estimated at 7-day intervals, and we reported the median and 95% credible interval (cri). (figure 3 ). during the second wave, the doubling time in seoul decreased to 6.0 (95% ci: 5.4, 6.7) days, indicating faster transmission compared to that during the first wave ( table 1) . as of 15 july 2020, the rt in seoul was estimated at 0.9 (95% cri: 0.7-1.2), straddling the epidemic threshold of 1.0, and suggesting potential for further transmission of the virus. gyeonggi province (literally meaning the "province surrounding seoul") is located in the western central region of korea and is the most populous province in south korea with a population of 13.5 million people. in gyeonggi province, the daily number of new cases by date of symptoms onset during the last weeks of february was 6.3 on average (figure 4) . accordingly, the first peak of rt occurred on 22 february, reaching 8.9 (95% cri: 4.8-14.2), with an estimated doubling time of 4.6 (95% ci: 4.2, 5.5) days (table 1) (50), door-to-door sales in the seoul metropolitan region (32), and yangcheongu sports facility (28). as of 19 july, the number of local cases in gyeonggi province was 1,027 (10.4% of the total reported cases in south korea), including 29 deaths, with an rt estimated at 0.8 (figure 4) . the incidence rate in the province was estimated at 108 per million. the first case in the sincheonji cult cluster (the largest covid-19 cluster in south korea) appeared on 18 february, resulting in sustained transmission chains, with 39% of the cases associated with the church cluster in gyeongbuk province. therefore, the virus alert level was raised to "red" (the highest level) on 23 february, and health authorities focused on halting the spread of the virus in daegu and gyeongbuk provinces. figure 5 shows that the peak of the epidemic occurred in the first week of march (with a reproduction number greater than one until 9 march) ( figure 5 ). the doubling time in gyeongbuk province reached the values as short as 3.6 (96% ci: 3.5, 4.0) days ( table 1) (figure 6 ). the estimates of the transmission potential of covid-19 in korea displayed substantial spatiotemporal variation. indeed, several factors influence the value of the reproduction number, including the transmissibility of an infectious agent, individual susceptibility, individual contact rates, and control measures (anderson and may, 1991) . our results indicate that the effective reproduction number for covid-19 declined to low levels after the first wave and straddled around the epidemic threshold of 1.0 in march and april suggesting that social distancing measures had a significant effect on mitigating the spread of the novel coronavirus. estimates of early national rt for south korea retrieved from other studies, 2.9 (95% cri 2.0-3.9) in february (ryu et al., 2020) and 2.6 (95% ci: 2.3-2.9) in march, are in good agreement with our rt estimates (zhuang et al., 2020) . our results suggest that south korea has experienced two spatially heterogenous waves of the novel coronavirus. at the regional level, seoul and gyeonggi province have experienced two waves whereas daegu and gyeongbuk provinces are yet to experience the second wave of the disease. the highest epidemic peak occurred in daegu and gyeongbuk province in late february and early march, with rt estimated at 4.4 (95% cri: 2.6-6.6) and 3.5 (95% cri: 0.9-7.3), respectively. during their epidemic peak, the doubling time was estimated at 2.8 (95% ci 2.5, 4.0) days and 3.6 (95% ci 3.5, 4.0) days in daegu and gyeongbuk province, respectively, which is similar to prior estimates of doubling time, 3.8 (95% ci: 3.4-4.2) days (lee et al., 2020) . similarly, in gyeonggi province and seoul, the first wave was observed in late february and early march, respectively. however, sporadic clusters of infections appeared in seoul and near gyeonggi province, immediately after the government eased its strict nationwide social distancing guidelines on may 6. this resurgence of infections in seoul and gyeonggi province (i.e., the province surrounding seoul) after a sustained period with fewer than 5 cases per day in each region, led to j o u r n a l p r e -p r o o f the second epidemic wave with sub-exponential growth dynamics. in seoul, the mean doubling time decreased from 7.5 (95% ci: 7.0, 8.2) days during the first wave to 6.0 (95% ci: 5.4, 6.7) days during the second wave, indicating faster transmission during the case resurgences. accordingly, our findings revealed sustained local transmission in seoul and gyeonggi province, with the estimated reproduction number estimated above one until the end of may. in late may, the country implemented two weeks of strict social distancing measures incorporating stringent virus prevention guidelines for the metropolitan area. these measures included the shutting down of public facilities and regulating bars and karaoke rooms. in the second week of june, south korea decided to indefinitely extend a period of strict social distancing measures, as nearly all locally transmitted cases were in the metropolitan area. although korea has a relatively low number of reported cases compared to other countries including the u.s. and china, it is believed that south korea is currently experiencing yet another resurgence of the virus (who). originally, south korean authorities predicted a resurgence of the virus in the fall or winter; however, this possible second wave started in and around seoul, which, with 51.6 million inhabitants, accounts for about half of the entire population of the country. secondary waves of the disease can result from multiple factors, including easing of travel restrictions and resuming social activities especially in the high population density areas of seoul and gyeonggi province. furthermore, a substantial proportion of covid-19 cases are asymptomatic (mizumoto et al., 2020) ; thus, they are not detected by surveillance systems, resulting in the underestimation of the epidemic growth curve. it was also recently reported that individuals aged 20-39 years in south korea drove the covid-19 epidemic throughout society with multiple rebounds, and an increase in infection among the elderly was significantly associated with an elevated transmission risk among young adults (yu et al., 2020) . our study is not exempt of limitations including the lack of dates of symptoms onset for all of the cases, relying on a statistical reconstruction of the epidemic curve by dates of symptoms onset as in a previous study (shim et al., 2020a) . overall, using most up-to-date epidemiological data from south korea, our study highlights the effectiveness of strong control interventions in south korea and j o u r n a l p r e -p r o o f contributions: es conceptualized analysis, retrieved and managed the data. es, gc, and at analyzed the data. es and gc wrote the first draft of the paper. all authors contributed to the writing of the paper. coronavirus: south korea confirms second wave of infections infectious diseases of humans: dynamics and control on the 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severity of covid-19 in south korea assessing reporting delays and the effective reproduction number: the ebola epidemic in drc different epidemic curves for severe acute respiratory syndrome reveal similar impacts of control measures distinctive trajectories of the covid-19 epidemic by age and gender: a retrospective modeling of the epidemic in south korea preliminary estimates of the reproduction number of the coronavirus disease (covid-19) outbreak in republic of korea and italy by 5 table 1. regional variations in doubling times in days of covid-19 cumulative incidence and its 95% j o u r n a l p r e -p r o o f key: cord-324231-nik7xizn authors: aitsi-selmi, amina; murray, virginia; heymann, david; mccloskey, brian; azhar, esam i.; petersen, eskild; zumla, alimuddin; dar, osman title: reducing risks to health and wellbeing at mass gatherings: the role of the sendai framework for disaster risk reduction date: 2016-04-07 journal: int j infect dis doi: 10.1016/j.ijid.2016.04.006 sha: doc_id: 324231 cord_uid: nik7xizn mass gatherings of people at religious pilgrimages and sporting events are linked to numerous health hazards, including the transmission of infectious diseases, physical injuries, and an impact on local and global health systems and services. as with other forms of disaster, mass gathering-related disasters are the product of the management of different hazards, levels of exposure, and vulnerability of the population and environment, and require comprehensive risk management that looks beyond single hazards and response. incorporating an all-hazard, prevention-driven, evidence-based approach that is multisectoral and multidisciplinary is strongly advocated by the sendai framework for disaster risk reduction 2015–2030. this paper reviews some of the broader impacts of mass gatherings, the opportunity for concerted action across policy sectors and scientific disciplines offered by the year 2015 (including through the sendai framework), and the elements of a 21(st) century approach to mass gatherings. mass gatherings of people at religious pilgrimages and sporting events are linked to numerous health hazards and accidents. [1] [2] [3] [4] traditionally, attention from public health authorities has focused on the transmission of infectious diseases, their impact on local health systems and services, and the threat to global health security of those with epidemic potential. [5] [6] [7] the world health organization (who) defines a mass gathering as ''an organized or unplanned event where the number of people attending is sufficient to strain the planning and response resources of the community, state or nation hosting the event''. 8 events at religious pilgrimage sites, sports facilities, air shows, musical festivals, political rallies, and other events that attract crowds vary in their complexity and demand for medical services and can lead to losses in lives, livelihoods, and health in the event of failure to cope with health hazards in emergency situations. 9 one of the largest regular mass gatherings in the world is the hajj. 1 it is the annual mass gathering of over two million muslims from all over the world and presents challenges to the authorities in saudi arabia. 1, 10 the inevitable overcrowding in a confined area of such large numbers increases the risk of injuries, 11 heat exposure, 12 and a range of infectious diseases. the risk of infection was evident in the outbreaks of meningococcal w135 strains in 2000 and 2001 with their associated high mortality and potential for international spread. 10 indeed, the annual hajj has faced several disasters due to fires at camp sites and in crowded tunnels, falling cranes, and stampedes due to failures in crowd movement control. 13 however, as in a number of other health policy areas, reducing the health risks of mass gatherings and seizing the opportunities for health improvement that mass gatherings may offer requires a broader approach to the underlying determinants of risk. 1 a comprehensive risk approach incorporates a wide range of hazards as well as taking into account the role of population vulnerability and exposure levels. 9, 14, 15 such an approach is akin to the social determinants of health approach, which looks at the upstream factors behind health outcomes, including socioeconomic inequalities. 16 the positive implication of this more comprehensive approach is that mass gatherings, as with other forms of hazard, can be seen as amenable to prevention, and new avenues of policy and management to reduce the risk to people and their environment open up. there is global agreement that disasters are not natural events and that disaster risk arises as the result of the interaction between hazards (natural hazards such as earthquakes or human-made hazards such as anthropogenic climate change) and predisposing vulnerabilities and exposures. disaster risk reduction (drr) encompasses the scientific, policy, and practice activities that aim to reduce losses in lives, livelihoods, and health by acting on hazard probability, vulnerability, and exposure levels. 17 as alluded to above with the hajj example, the health consequences of mass gathering-related disasters are many and go beyond the transmission of travel-related infectious disease (middle east respiratory syndrome coronavirus (mers-cov), severe acute respiratory syndrome (sars), etc.). they include injuries resulting from crowd density and inadequate infrastructure (e.g., bridge collapse), exposure to extreme weather events, and escalation of violence as a result of crowd behaviour. 18 risks can be compounded, for example, when population displacement and overcrowding in evacuation or re-housing facilities leads to a further increase in the risk of infectious disease outbreaks, or overwhelmed medical services are unable to deliver on elective functions such as chronic disease management, putting those who need life-saving medication such as insulin for diabetes in a particularly vulnerable position. 19, 20 furthermore, the mental health consequences of traumatic incidents such as disasters, in general, can be prolonged, with stress to people, families, and communities resulting in short-term fear of death, 21 as well as general distress, anxiety, excessive alcohol consumption, and other psychiatric disorders. 22 in other words, mass gatherings, if improperly managed, can result in what has been defined by the united nations international strategy for disaster reduction (unisdr) as ''a serious disruption of the functioning of a community or a society involving widespread human, material, economic or environmental losses and impacts, which exceeds the ability of the affected community or society to cope using its own resources'' -the unisdr's definition of a disaster. 17 the sendai framework for disaster risk reduction 2015-2030 is the first of three united nations landmark agreements agreed in 2015 (the other two being the sustainable development goals (https://sustainabledevelopment.un.org/) agreed in september 2015, and the un framework convention on climate change adopted in december 2015 (http://unfccc.int/2860.php)). 23 the sendai framework is a voluntary agreement adopted on march 18, 2015 by 187 united nations member states after extensive negotiations at the world conference on disaster risk reduction, the successor to the hyogo framework for action 2005. it has a greater emphasis on health and gives a clearer mandate emphasizing the need for more integrated drr that incorporates bottom-up as well as top-down approaches, local scientific and technical knowledge, and draws attention to synergies with other critical policy arenas, including health, climate change, and sustainable development. 24 the sendai framework captures the developments in science and policy thinking of the last 10-20 years in moving beyond a single hazard and a response-focused approach to disasters, to an all-hazard, preventive, multisector and multidisciplinary approach that links with sustainable economic development and climate change. 25 the sendai framework outcome for the next 15 years is to achieve ''the substantial reduction of disaster risk and losses in lives, livelihoods and health and in the economic, physical, social, cultural and environmental assets of persons, businesses, communities and countries''. the following actions with a public health focus are agreed in the sendai framework with local, national, regional, and global partners as relevant: ''enhancing the resilience of national health systems through training and capacity development; strengthening the design and implementation of inclusive policies and social safety-net mechanisms, including access to basic health care services towards the eradication of poverty; finding durable solutions in the post-disaster phase to empower and assist people disproportionately affected by disasters, including those with life-threatening and chronic disease; enhancing cooperation between health authorities and other relevant stakeholders to strengthen country capacity for disaster risk management for health; the implementation of the international health regulations (2005) and the building of resilient health systems; improving the resilience of new and existing critical infrastructure, including hospitals, to ensure that they remain safe, effective and operational during and after disasters, to provide live-saving and essential services; establishing a mechanism of case registry and a database of mortality caused by disaster to improve the prevention of morbidity and mortality and enhancing recovery schemes to provide psychosocial support and mental health services for all people in need''. 23 the sendai framework also recognizes the challenges and gaps: ''enhanced work to reduce exposure and vulnerability, thus preventing the creation of new disaster risks, and accountability for disaster risk creation are needed at all levels. more dedicated action needs to be focused on tackling underlying disaster risk drivers, such as the consequences of poverty and inequality, climate change and variability, unplanned and rapid urbanization, poor land management and compounding factors such as demographic change''. 23 the sendai framework has a strong emphasis on the importance of science as a robust foundation for informing decisionmaking and underpinning drr. specific recommendations for the scientific community to improve the understanding of risk and how to achieve its expected outcome of reducing disaster losses in lives, livelihoods, and health include: ''enhanced scientific and technical work on disaster risk reduction and its mobilization through the coordination of existing networks and scientific research institutions at all levels and all regions, with the support of the united nations international strategy for disaster reduction's scientific and technical advisory group, in order to strengthen the evidence base in support of the implementation of this framework; promote scientific research of disaster risk patterns, causes and effects; disseminate risk information with the best use of geospatial information technology; provide guidance on methodologies and standards for risk assessments, disaster risk modelling and the use of data; identify research and technology gaps and set recommendations for research priority areas in disaster risk reduction; promote and support the availability and application of science and technology to decision-making; contribute to the update of the terminology on disaster risk reduction; use post-disaster reviews as opportunities to enhance learning and public policy and disseminate studies''. 23 the sendai framework, when implemented, has the potential to be a truly relevant framework for health, advocating for an allhazards approach. it makes more than 30 explicit references to health, highlighting the importance of outbreaks and epidemics, chronic disease management, psychosocial interventions, rehabilitation as part of disaster recovery, and makes several references to the international health regulations. reducing losses in lives, livelihoods, and health: building on synergies between disaster risk reduction and health to reduce risks from mass gatherings the battle against the spread of travel-related infections and other risks facilitated by globalization that arise from mass gatherings is a shared responsibility between different countries, sectors, and disciplines that can help to reduce risk. the coordination of preventive measures by health services, emergency services, engineers, scientists, the private sector, governments, and civil society requires the adoption of an all-hazard approach that is multidisciplinary and multisectoral. the benefits from such measures go beyond those directly involved in any particular mass gathering to protect health and reduce vulnerability globally. the expansion of drr from a (single) hazard response-focused approach to a risk-based approach addressing vulnerability and exposure alongside hazard probability has been compared to the widening of the scope of health activities beyond clinical interventions on diseases to health system strengthening and prevention. public health is increasingly concerned with the latter and works across policy sectors that have an impact on health and wellbeing, such as economic, agricultural, and educational policy. an important driver is the realization that the costs of reactive health interventions dealing with illness in hospitals are exceeding societal resources, alongside concerns for fairness and equity. 16 given the health imperative for drr over the 2015-2030 period, as promoted in the sendai framework, a much stronger focus on improving the health outcomes for people at risk of emergencies is needed. through participation in the sendai framework policy process, health actors and their partners such as the unisdr have worked to ensure that people's health is considered as an explicit outcome of the sendai framework and that health outcomes are seen as a shared responsibility among all actors in drr and emergency risk management. 26, 27 member states of the who made high-level policy commitments to drr and adopted a resolution at the 2011 world health assembly to strengthen national health emergency and disaster management capacities and the resilience of health systems. 28 looking to the future, member states and the who secretariat have set a course that brings together drr and emergency response. commitments include the provision of greater input and participation by the health sector in drr national, regional, and global fora. the who promotes an all-hazard approach 29 and an integrated multisectoral response to emergencies. 26 the who global pandemic influenza preparedness framework (http://www. who.int/influenza/resources/pip_framework/en/) has already embraced the principles of this integrated all-hazard approach. a conceptual diagram for the integration of the who emergency and disaster risk management for health (edrm-h) framework into broader national drr strategies has been proposed (see figure 1 ), 30, 31 and could potentially be used to guide the risk management of large mass gathering events. following the adoption of the sendai framework, the who has committed to building on previous efforts and is currently developing guidance (''reducing health consequences of emergencies and disasters: a risk management policy guide'') to help countries to effectively manage emergency risks and reduce their health consequences. 27 mass gatherings can introduce new and challenging risks that need to be managed and need to be understood better. 32 priority 4 of the sendai framework calls for the drr community and its partners: ''[t]o develop and strengthen, as appropriate, coordinated regional approaches and operational mechanisms to prepare for and ensure rapid and effective disaster response in situations that exceed national coping capacities''. the health sector has clearly recognized the link between mass gatherings and preparedness to reduce disaster risk, but the translation of global policy into local and national capacity remains to be achieved. the sendai framework offers an opportunity to galvanize member states and local authorities to achieve common goals by offering a clearer vision and narrative for concerted action and funding reform. the sendai framework offers a unique opportunity to move beyond simply responding to emergencies to a more comprehensive, prevention-based approach to mass gathering management through the use of science and technical capabilities. it puts the protection of people's health, lives, and livelihoods at its centre. of note, the sendai framework promotes the strengthening of the science-policy interface and the development of links to other large global instruments (sustainable development goals, climate change, and the international health regulations). in summary, globalization has created interdependencies that render local disaster impacts in distant locations relevant to communities everywhere, such that risk is shared across national and institutional boundaries. therefore, reducing risk is a shared responsibility particularly where events or mass gatherings are enhanced by the advantages of globalization in terms of travel, interconnectivity of services, and supply chains. 33 for an evidencebased approach to the health impacts (including infectious disease control) of mass gatherings to be effective, it will be important to blend all-hazard risk management strategies across current global initiatives. in practice, for countries, this will mean harmonizing national strategies across intergovernmental agreements, including the sendai framework, the international health regulations, the sustainable development goals, and the un framework convention on climate change, to optimize resource investment. conflict of interest: the authors declare that they have no conflicts of interest. report: science is used for disaster risk reduction hajj: infectious disease surveillance and control olympic and paralympic games: public health surveillance and epidemiology european football championship finals: planning for a health legacy global perspectives for prevention of infectious diseases associated with mass gatherings emerging infectious 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their families involved in war and disasters mental health effects of hurricane sandy: characteristics, potential aftermath, and response the sendai framework for disaster risk reduction the sendai framework for disaster risk reduction: renewing the global commitment to people's resilience, health, and well-being from knowledge to action: bridging gaps in disaster risk reduction world health organization. statement made at the global platform for disaster risk reduction world health organization. who statement to the 4th session of the global platform for disaster risk reduction strengthening national health emergency and disaster management capacities and resilience of health systems who's interdepartmental mass gatherings group best practice protecting people's health from the risks of disasters integrating health into disaster risk reduction strategies: key considerations for success world health organization the impacts of natural disasters on global supply chains key: cord-355343-dtdsd8j2 authors: buonsenso, danilo; cinicola, bianca; raffaelli, francesca; sollena, pietro; iodice, francesco title: social consequences of covid-19 in a low resource setting in sierra leone, west africa date: 2020-06-01 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.104 sha: doc_id: 355343 cord_uid: dtdsd8j2 economical and psychological consequences of the lockdown in low-resource setting in rural africa are unknown. we drafted a survey in order to address the social impact of covid-19 lockdown on a rural village in sierra leone. the survey developed by the study group and translated in the local language, distributed to the householders of the village on april 13(th) and responses collected on april 14(th), when sierra leone was on day 11 of lockdown. the questions aimed to assess in the community the following items: age group, main activities before lockdown, change in income and ability to feed the family during lockdown, anxiety during lockdown. 78 householders (100% of bureh town) replied. all, expect one, declared a 51-80% (19.2%) to 81-100% (79.4%) reduction of weekly income compared with the pre-lockdown period, declaring difficulties in providing food for the family members (82%), and anxiety (60%). our analyses showed that people lost their jobs and have difficulties in providing food for their families. liberia were closed; on april 3rd a three-day lockdown started and eventually on april 8th, due to the local escalation in reported cases, a 14-day lockdown was released, with the possibility of extension according to the epidemiological development. despite these restrictions, on april 18th, 30 confirmed cases were reported, 532 people put in quarantine but still zero deaths related j o u r n a l p r e -p r o o f to covid-19 were documented. economical and psychological consequences of the lockdown in low resources setting in rural africa are worrying the experts of global health (el-sadr et al. 2020), but are still unknown and their early analysis will allow corrective interventions or preventive measures to support fragile areas to minimize the impact on the population. we drafted a survey in order to urgently address the social impact of covid-19 lockdown on the rural village of bureh town, sierra leone, west africa (figure 1) and quickly implement corrective measures. it was developed in english by the lead author, reviewed by the research team and translated in the local language by the headman and the authors of this study. the headman represent the chief of rural areas in sub-saharan west africa, being comparable as a mayor of city in high resource countries. the survey had been deliberately made simple so that everyone could respond regardless of schooling and included questions on age of the respondents, number of people and age groups of people living in the house, work situation and weekly income before and after the lockdown. the administered survey was composed with a descriptive purpose and composed of detailed questions aimed to assess the following items in the community: age group, main activities before lockdown, change in income and ability to feed the family during lockdown, anxiety during lockdown (supplementary material). the survey was a clinical/demographic one with descriptive aims. (table 1) , representing a total of 560 bureh town citizens (142 children under 5; 75 aged between 6 and 15; 80 aged between 16 and 25; 186 aged between 25 and 40, 75 aged between 40 and 60; 12 aged more than 60 years). all people were dependent from the local stream to collect water, where the younger groups of the family go every morning for this issue. people were involved in local jobs such as: fishing (20, 25.7%), tourism (18, 23.1%), marketing (81 10.2%), schoolteacher (4, 4.1%), others (8, 10.2%) while 20 (25.7%) declared not to have a job before the lockdown. all householders, expect one, declared a 51-80% (15 householders, 19.2%) to 81-100% (62 householders, 79.4%) reduction of weekly income compared with the pre-lockdown period, declaring difficulties in providing food for the family members in 82% of respondents, due to lack of economic resources related to the reduced income and activities related to the lockdown; 76.9% of respondents declared to be very worried about economic fallout from the lockdown with 60% of householders declaring a mild-moderate anxiety. our analyses, even if just focused on a small village, showed a profound indirect impact of sars-cov-2 spread in sierra leone. considering the rapid worldwide diffusion of coviddramatic health impacts (of note only one ventilator is available for the whole population of sierra leone). lockdown seemed to be the only measure to delay contagion but this decision was not without consequences for people, especially those living in fishing and touristic areas of the country. in our survey, all people but one declared a 51% to 100% reduction of weekly income with consequences in the ability to provide food for the family members, thus confirming results by other studies (dyer 2020) . most of the respondents considered themselves worried j o u r n a l p r e -p r o o f about the situation with a mild percentage of the population living in a mild-anxiety state. in fact, the households provided the response on day eleven since first lockdown was declared, meaning that local touristic activities, as well as minor markets, were already affected, with economic consequences for local workers, by more than seven days. these results are probably due to the fact that, differently from governments of high-income countries, community members were not supported by the administrations. for example, in the european union and the united states, the government pushed the economy providing billions of euros/dollars to support those families that lost jobs or whose income was severely affected by the reduced business. the findings of our survey confirm the fear of severe consequences of the spread of sars-cov-2 in sub-saharan africa and the need for special surveillance tools(el zowalaty and järhult 2020). although kapata et al.(kapata et al. 2020) gave a positive answer to the question "is africa prepared and equipped to deal with yet another outbreak of a highly infectious disease -covid-19?", our data suggest that community members is economically and then psychologically suffering from this situation. certainly, substantial progresses has been made in africa since the 2014-16 ebola outbreak (delamou et al. 2017) , with lessons learned from previous and ongoing outbreaks (largent 2016; omoleke et al. 2016 preparedness and response to pediatric covid-19 in european emergency departments: a survey of the repem and peruki networks public health impact of the 2014-2015 ebola outbreak in west africa: seizing opportunities for the future building resilience against biological hazards and pandemics: covid-19 and its implications for the sendai framework covid-19: africa records over 10 000 cases as lockdowns take hold africa in the path of covid-19 from sars to covid-19: a previously unknown sars-cov-2 virus of pandemic potential infecting humans -call for a one health approach. one health is africa prepared for tackling the covid-19 (sars-cov-2) epidemic. lessons from past outbreaks, ongoing pan-african public health efforts, and implications for the future ebola and fda: reviewing the response to the 2014 outbreak, to find lessons for the future ebola viral disease in west africa: a threat to global health, economy and political stability a novel coronavirus from patients with pneumonia in china we are thankful to the local operators of bureh village: ismail jaber, matilda yamba, prince williams, memunatu n kallon, nee turay. we are also grateful to all our colleagues that j o u r n a l p r e -p r o o f key: cord-347349-caz5fwl1 authors: yu, xinhua; duan, jiasong; jiang, yu; zhang, hongmei title: distinctive trajectories of covid-19 epidemic by age and gender: a retrospective modeling of the epidemic in south korea date: 2020-07-02 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.101 sha: doc_id: 347349 cord_uid: caz5fwl1 objectives: elderly people had suffered disproportional burden of covid-19. we hypothesized that males and females in different age groups might have different epidemic trajectories. methods: using publicly available data from south korea, daily new covid-19 cases were fitted with generalized additive models, assuming poisson and negative binomial distributions. epidemic dynamics by age and gender groups were explored with interactions between smoothed time terms and age and gender. results: a negative binomial distribution fitted the daily case counts best. interaction between the dynamic patterns of daily new cases and age groups was statistically significant (p < 0.001), but not with gender group. people aged 20-39 years led the epidemic processes in the society with two peaks: one major peak around march 1 and a smaller peak around april 7, 2020. the epidemic process among people aged 60 or above was trailing behind that of younger people with smaller magnitude. after march 15, there was a consistent decline of daily new cases among elderly people, despite large fluctuations of case counts among young adults. conclusions: although young people drove the covid-19 epidemic in the whole society with multiple rebounds, elderly people could still be protected from virus infection after the peak of epidemic. the novel severe acute respiratory syndrome associated beta-coronavirus (sars-cov-2) of unknown origin, appeared in wuhan, china in late december 2019 and has swept the world over the past few months (anderson et al. 2020; li et al. 2020a; zhu et al. 2020) , causing over 491,500 deaths worldwide (https://coronavirus.jhu.edu/map.html, accessed on june 26, 2020) and significantly disrupting both societal activities and person life (center 2020) . although several early studies described the dynamics of the epidemic process in details (li et al. 2020a; wu and mcgoogan 2020) , many uncertainties remained. for example, diagnosis criteria varied significantly across countries. during the early epidemic in wuhan, china, patients were required to have serious pneumonia symptoms plus lab confirmed virus detection (huang et al. 2020; zhu et al. 2020) , thus missing most mildly symptomatic and all asymptomatic patients. as suggested in a modeling study, probably 86% of covid-19 cases might be undocumented in wuhan (li et al. 2020b) . many epidemic measures such as basic reproduction number based on early epidemic in wuhan were questioned by later studies due to possible underestimating the true parameters (nishiura et al. 2020; zhao et al. 2020a; zhao et al. 2020b ). on the other hand, some countries such as south korea and singapore classified patients only based on lab tests, yielding a better picture of the epidemic. to fully understand the epidemic process of covid-19, accurate and complete epidemic data are indispensable. data from south korea have been generally considered of highest quality, mainly due to two notable strategies adopted by the south korea government from the beginning of the epidemic: extensive contact tracing and massive testing to identify possible cases in addition to case isolation (shim et al. 2020) . south korea identified the first covid-19 case on jan 20, 2020, and the outbreak started its exponential growth after feb 19, 2020. in an outbreak j o u r n a l p r e -p r o o f occurred in a call center, 1,143 people were tested, 97 were positive and confirmed (positive rate 8.5%) (park et al. 2020) . after tracing all contacts of those 97 cases, about 16% were tested positive (secondary attack rate). in addition, south korea also installed roadside testing stations to test any person who had concerns about his/her infectious status, in addition to those who had contacted known patients. such extensive controlling measures not only halted the epidemic successfully but also produced a more complete picture of the covid-19 epidemic. a striking phenomenon in covid-19 was that people aged 65 or older suffered the heaviest burden of the disease (richardson et al. 2020; wu and mcgoogan 2020) and the proportion of cases was higher in men than that of women. according to a recent cdc report, about 80% of deaths occurred among elderly people, and those aged 80 or above had almost 15% chance of dying if infected (cdc 2020; garg et al. 2020) . in our previous analysis based on florida covid-19 data, we found that people aged 65 or older accounted for 54% of hospitalizations and 82% of deaths. the mortality rate was 14% among elderly people who were infected with coronavirus (yu 2020a). furthermore, since may 1, 2020, the covid-19 pandemic has been waning down across the world (https://coronavirus.jhu.edu/map.html), pressing many countries to consider re-opening the business. many public health experts warned a possible rebound of new cases if current interventions were relaxed (chowell and mizumoto 2020; ferguson et al. 2020; kissler et al. 2020 ). a recent model predicted that covid-19 epidemic might last more than a year and multiple waves of outbreaks were possible (kissler et al. 2020) . it is likely elderly people may still suffer the heaviest disease burden during the return of outbreak (hay et al. 2020 ). however, it was unknown whether and how the epidemic processes were different between young and old people. in this study, we aim to statistically learn the dynamics of the covid-19 j o u r n a l p r e -p r o o f pandemic based on data from south korea. in addition to identifying the best fit of the epidemic process, we explore gender-and age group-specific trajectories of covid-19 to facilitate our understanding of the disease and its impact on different populations, and inform the potential and severity of covid-19 rebound. the daily counts of confirmed new covid-19 cases and deaths were obtained from the open source (https://github.com/jihoo-kim/data-science-for-covid-19, accessed on may 2, 2020), which were systematically gathered from korea center for disease control (kcdc) daily reports. all cases were verified against kcdc reports. the line list file included patient's age, gender and date of virus infection confirmation. however, the line list file excluded almost all cases occurred in the city of daegu (more than 6,000 cases), and thus cases from daegu were excluded from our study. we further excluded cases with missing confirmation date (n=3). age was grouped (in years) as 0-19, 20-39, 40-59, and 60 or above. those with missing gender information (n=78) or missing age information (n=86) were retained in the analysis for overall trajectories (total sample size n=3349), but were excluded in the gender or age specific analysis. since our purpose in this study was not to predict new cases in the future but to model the epidemic process, we adopted a semi-parametric generalized additive model (gam) to obtain fitted daily case counts and also account for non-linear patterns of epidemic process (wood 2017) . the time was modeled as a continuous variable with smoothing terms (thin plate regression splines with 8 knots). interactions between smooth terms and gender (or age group) j o u r n a l p r e -p r o o f were modeled as separate smoothing function for each group. specifically, for interaction models: where yij represents the observed case counts of day i and group j that follows a certain distribution. in this study, we focused on negative binomial (nb) or poisson distributions due to their robustness. we use variable timei to represent day starting from 1, ij( ) is an indicator variable (0/1) denoting if daily counts of new cases is for group j (1) or not (0), bk( ) represents a basis function for the k th term to smooth temporal trend, and j,k are regression coefficients for smooth term k and group j (representing group-specific effects). parameters were estimated via the restricted maximum likelihood (reml) approach. the generalized cross validation criterion with mallows' cp (gcv.cp) and maximum likelihood (ml) methods were also explored. therefore, the above gam framework allows us to compare different trajectories through examining the interactions between smoothed time term and age/gender groups with a focus on comparing the overall trajectories rather than point-wise comparisons. statistics r 2 and percent of deviance explained by the models were used to identify the best fit model. r package mgcv was used to fit the gam model (wood 2017) . the data and programs are available online at https://github.com/jiasong-duan/covid-19-epidemic-trajectories. from feb. 19 to apr. 30, 2020, there were 3,349 covid-19 cases (1,439 males, 43%) identified outside the daegu city. those with age 0-19 accounted for 6% (n=202) of total cases, and age j o u r n a l p r e -p r o o f 8 20-39 for 37% (n=1,227), age 40-59 for 31% (n=1,034), while those with age 60 or above accounted for 24% (n=800) of total cases. as shown in figure 1 , the epidemic outside the daegu city peaked around mar. 1, 2020 and declined afterwards except for a second small peak around march 28, 2020. the fitted curves to the observed daily new cases were overlaid on the observed counts in figure 1 . predictions from both nb and poisson models were indistinguishable. however, the confidence intervals from nb model were much wider than that of poisson model. as shown in the model comparison to be conservative, the model based on nb distribution was selected and implemented in the subsequent analyses. the confidence intervals from the fitted models were omitted in the subsequent plots to emphasize different overall patterns in the epidemic process. while there were two peaks in the epidemic process among people aged 20-39 years. in fact, the epidemic among people aged 20-39 led the whole epidemic process in the total population such that not only did young adults have more daily new cases than that of other age groups, but also the epidemic processes among people aged 40-59 and 60+ years were trailing one to three days behind that of aged 20-39. to further explore age and gender effects on the epidemic process, figure 3a -b presented the fitted epidemic curves by age groups for males and females separately. among males, people aged 20-39 had highest predicted daily counts and experienced two peaks over time, while those aged 60 or older had much lower daily case counts and decreased consistently over time despite the large changes of epidemic in young adults. those aged 40-59 also experienced two peaks in the epidemic but were at a smaller scale than young adults. the patterns of epidemic processes by age groups among females were different from that of males. those females aged 40-59 and aged 20-39 had similar epidemic processes during the first peak of epidemic. the daily case counts among females aged 20-39 also increased after april 1, 2020. females aged 60 or above had smaller magnitude of epidemic but overall, similar to that of females aged 40-59. in this study, we demonstrated different trajectories of covid-19 epidemic between gender and age groups based on south korea data. first, based on case reporting date and assuming similar incubation periods and reporting delays across all groups and over the whole study period, young people aged 20-39 years led the epidemic processes in the whole society and also had j o u r n a l p r e -p r o o f experienced two peaks about one-month apart, one major peak around march 1 and a smaller peak around april 7, 2020; second, school age people (aged 0-19) had much smaller magnitude of epidemic overall; and finally, the epidemic process among people aged 60 or above was trailing behind that of younger people, and the magnitude of epidemic was smaller than that of people aged 20-39 or 40-59. after march 15, there was a steady decline of daily new cases among people aged 60 or above, despite large fluctuations of case counts among young adults. our findings were consistent with other reports in which younger people accounted for most confirmed covid-19 cases (guan et al. 2020; wu and mcgoogan 2020; zhang et al. 2020 ). our empirical evidence from high quality data supported that covid-19 epidemic was driven by the infection among young adults. in addition, school age children had the least burden of disease, possibly due to early school closure and vacation breaks during that period. this pattern was different from that of typical respiratory infection diseases such as seasonal flu in which most cases were school age children. worldwide, people aged 60 or above endured a disproportional burden of covid-19 disease (wu and mcgoogan 2020) . they had a higher risk of hospitalizations, and about 80% deaths occurred in this age group (garg et al. 2020 ). however, it was unclear whether elderly people were more likely to get infected, whether virus transmissibility was higher among elderly, or whether elderly people were merely more likely to have severe diseases than younger people (hay et al. 2020; zhang et al. 2020) . elderly people generally have weaker immune system than younger people. meanwhile, they have been exposed to many viruses over lifetime that may shield them from getting infected by a new virus, but there was no evidence for any prior immunity to the sars-cov2. nonetheless, our findings provided some hope for mitigating the impact of epidemic on this vulnerable population. as demonstrated in figure 2b and 3a in addition, although overall gender difference in the covid-19 epidemic was moderate, age and gender specific analyses suggested that females (and to a less extent, males) aged 40-59 had similar experience of epidemic to that of people aged 20-39. this might be because this age group often had close and frequent contacts with younger people in work or within households. though the risks of hospitalizations and deaths were low among this population, they were higher than that of regular respiratory infectious diseases such as seasonal flu. thus, the disease burden among this middle age group should not be neglected. there were some limitations in this study. first, our study excluded cases from the city of daegu (over 6000 cases) because detail information about cases from that city was not released to the public. although it was unlikely to bias our results, information from such a large outbreak could provide some additional insights on how the epidemic unfolded among people of different age and gender. however, during the early stage of epidemic, little gender and age stratified data j o u r n a l p r e -p r o o f were publicly available, and most individual level data from other regions were incomplete as well. second, we employed statistical methods to examine the trajectories of epidemic. there were two perspectives to model the epidemic process (hethcote 2000; unkel et al. 2012) . one common approach was to model the process based on the mechanisms of the epidemic. for example, the susceptible-exposed-infectious-removed (seir) model and its variants had been used to assess the dynamic of epidemic, obtain epidemic parameters, and evaluate the impact of various control measures on the epidemic (kucharski et al. 2020; peak et al. 2017; prem et al. 2020; yu 2020b) . agent-based models were also used to simulate the epidemic process and assess the effects of various interventions (ferguson et al. 2020; ). the other perspective was based on traditional statistical models. non-linear models such as generalized logistic growth model (chowell 2017 ) were used to model the growth of the epidemic and estimate the growth rate of cases over time. in addition, some researchers directly modeled the epidemic curve with regression techniques, assuming daily counts follow some distributions such as poisson or negative binomial distributions. for example, models based on time series of count data were adopted to predict the covid-19 deaths in the us, such as those models from institute of health metrics and evaluation (ihme) (ihme 2020) and university of texas-austin (woody et al. 2020). our previous research also used vector autoregressive models to examine the risk interactions across age groups after the peak of covid-19 epidemic (yu 2020c) . while there were many uncertainties among different gender and age groups about contact patterns, virus transmissibility and behavioral changes during the epidemic, since the epidemic data from south korea were more likely to be complete, it is possible to directly model the daily counts j o u r n a l p r e -p r o o f with regression models assuming a common distribution for count data. we believed that out models avoided many unfounded assumptions in the more complicated epidemic process models. third, we only have case reporting or lab confirmation dates in this study which were likely 3-5 days away from the actual virus infection date. the average incubation date for covid-19 was about 5 days (lauer et al. 2020 ) and the report delay in south korea was unknown but likely very short due to extensive testing. thus, we make some untestable assumptions in comparing epidemic trajectories between age and gender groups. the incubation period and reporting delay were assumed to be the same across all groups and over the whole study period. this should be pertinent in south korea as they started mass testing and contact tracing from the beginning of the epidemic (shim et al. 2020 ) but may not be appropriate for the regions that testing is severely limited and delayed. finally, we only analyzed data from south korea. the epidemic processes of covid-19 in different countries were likely different due to different population structure and different interventions to mitigate the epidemic (anderson et al. 2020; chowell and mizumoto 2020; hay et al. 2020; lipsitch et al. 2020) . meanwhile, we expect our findings provided a general picture of the epidemic trajectories of covid-19 and can serve as a reference to other regions. in addition, as witnessed in the covid-19 epidemic, politics and ideology often overtook science and public health, so that effective interventions were sometimes implemented too late and incomplete, leaving the public at lost and public health practitioners in conundrum. the main strength of our study was our straightforward analyses to explore different epidemic processes based on high quality data. insights often emerge through such modeling exercise. we stratified the models by age and gender groups and discovered their different trajectories in the epidemic. recent studies had predicted a long-lasting epidemic for covid-19 and possible j o u r n a l p r e -p r o o f multiple waves of outbreaks after societal re-opening (kissler et al. 2020) . our findings were unique in providing empirical evidence for designing effective public health strategies to mitigate the impact of recurrent covid-19 epidemics and protect vulnerable populations. in summary, in south korea, and likely in other countries, covid-19 epidemic processes had distinctive dynamic patterns among age and gender groups. epidemic among young adults led the epidemic process in the whole population, and a second peak occurred in people aged 20-39 years. more importantly, during the post-peak period of the covid-19 epidemic and in the process of gradually returning the society and economy to normalcy, elderly people could be protected effectively though case isolation, contact tracing, mass testing, and proper personal protections, as exemplified in south korea. dr. xinhua yu was supported by fedex institute of technology, university of memphis for conducting this research. this study used only publicly available data and no human subjects were directly involved, thus deemed to be exempted from the approval of institutional review board. no informed consent was needed. all authors declared no conflict of interest in conducting this study. how will country-based mitigation measures influence the course of the covid-19 epidemic? severe outcomes among patients with coronavirus disease 2019 (covid-19) -united states most americans say coronavirus outbreak has impacted 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number of the novel coronavirus disease (covid-19) during the early outbreak the basic reproduction number of novel coronavirus (2019-ncov) estimation based on exponential growth in the early outbreak in china from 2019 to 2020: a reply to a novel coronavirus from patients with pneumonia in china the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. key: cord-321412-6g3obmzc authors: khamis, faryal; al-zakwani, ibrahim; al hashmi, sabria; al dowaiki, samata; al bahrani, maher; pandak, nenad; al khalili, huda; memish, ziad title: therapeutic plasma exchange in adults with severe covid-19 infection date: 2020-06-23 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.064 sha: doc_id: 321412 cord_uid: 6g3obmzc objectives: to evaluate the therapeutic use of plasma exchange in covid-19 patients compared to controls. methods: case series of critically ill adult men and non-pregnant women, ≥18 years of age, with laboratory confirmed covid-19, was conducted at the royal hospital, oman, from april 17(th) to may 11(th), 2020. therapeutic plasma exchange (tpe) was performed on patients admitted to intensive care unit (icu) with confirmed or imminent acute respiratory distress syndrome (ards) or severe pneumonia. analysis was performed using univariate statistics. results: a total of 31 covid-19 patients were included with an overall mean age of 51 ± 15 years (range: 27-76 years), 90% (n = 28) were males, and 35% (n = 11) of the patients had tpe as a mode of treatment. the tpe group was associated with higher extubation rates than the non-tpe cohort (73% versus 20%; p = 0.018). additionally, patients on tpe had a lower 14 days (0 versus 35%; p = 0.033) and 28 days (0 versus 35%; p = 0.033) all-cause mortality compared to patients not on tpe. however, all-cause mortality was only marginally lower in the tpe group compared to the non-tpe group (9.1% versus 45%; p = 0.055; power = 66%). laboratory and ventilatory parameters also improved with the tpe. conclusions: the use of tpe in severe covid-19 patients has been associated with improved outcomes, however, randomized controlled clinical trials are warranted to draw final conclusive findings. the novel coronavirus ("sars-cov-2") pandemic continues to perpetuate globally with an estimated 7,930,989 cases and 433,783 pandemic by country and territory, 2020) deaths (as of june 15 th , 2020) without available effective treatment or vaccine. several randomized controlled clinical trials, in search of the cure, are in progress . the sars-cov-2 virus infects the respiratory epithelium of the lower airways, causing widespread damage via cytopathic effects, resulting in severe inflammation and pneumonitis. it is estimated that 13.8% of cases are severe and 6.1% are critical (who-china joint mission on coronavirus disease 2019 , 2020) that manifest as acute respiratory distress syndrome (ards), sepsis and /or multiorgan failure. the response to fulminant infection is characterized by excessive immune dysregulation (cytokine storm), inflammation, hypercoagulable state and endothelial dysfunction chang, 2019) . severe covid-19 disease has been associated with lymphopenia and high levels of ferritin, c-reactive protein (crp), lactate dehydrogenase (ldh), d-dimer and interleukin-6 (il-6) (xu et al., 2020) . recently, convalescent plasma containing protective antibodies, donated from survivors of covid-19 infection, has been shown as promising and safe treatment (joyner et al., 2020) . similarly, therapeutic plasma exchange (tpe), which is not a novel therapy, has been used in several studies for the management of severe infections such as 2009 hin1 influenza a, sepsis and multiorgan failure with a trend towards improved survival (knaup et al., 2018; busund et al., 2002; rimmer et al., 2014; patel et al., 2012; . moreover, tpe has been proposed as a possible supportive treatment for severe covid-19 infection and has been shown to be effective in a few case reports (shi et al., 2020; zhang et al., 2020) . we report here the results of tpe as a supportive/adjunct therapy for the management of covid-19 ards and severe pneumonia. the study was conducted at the royal hospital, a tertiary care hospital in muscat, oman, from april 17th, 2020 to may 11th, 2020. tpe was given after 7 and up to 14 days of illness to adult patients, 18 years of age, with laboratory confirmed covid-19 disease who were admitted to intensive care unit (icu) with confirmed or imminent respiratory failure and any one of the following conditions (ards definition task force, 2012): 1. ards was defined as acute-onset hypoxemia (the ratio of the partial pressure of arterial oxygen to the fraction of inspired oxygen [pao2:fio2], <300) with >50% bilateral pulmonary opacities on chest imaging within 24 to 48 hours that were not fully explained by congestive heart failure. j o u r n a l p r e -p r o o f 2. severe pneumonia in adults was defined as fever or suspected respiratory infection plus one of the following: respiratory rate of >30 breaths/ minute, severe respiratory distress and spo2 of <93% on room air. 3. septic shock in adults was defined as: persisting hypotension despite volume resuscitation, requiring vasopressors to maintain mean arterial pressure of ≥65 mmhg and serum lactate level of <2 mmol/l. 4. multiple organ dysfunction syndrome (mods) was defined as the progressive, potentially reversible, dysfunction of two or more organ systems following acute, life-threatening disruption of systemic homeostasis. we excluded pregnant women, patients with suspected or confirmed pulmonary embolism and patients with acute coronary syndrome. the study was approved by the royal hospital research and ethics committee (src#36/2020) and a written informed consent was obtained from the patient or (if intubated) through the health proxy. data collected included demographics, baseline characteristics, risk factors, sequential organ failure assessment (sofa) score, respiratory parameters ( fio2, peep, po2/fio2) pre plasma exchange (day 0) and post plasma exchange (day 7), laboratory parameters pre-plasma exchange (day 0) and post-plasma exchange (day 7), (absolute lymphocytic count (alc), crp, ldh, ferritin, d-dimer, il-6, ph and lactate), radiological features and clinical outcomes including icu length of stay, total length of stay, extubation and mortality rates at day 14 and day 28 post-plasma exchange as well as all-cause mortality. the data was compared with the medical records of 21 patients admitted from april 17 th to may 11 th , 2020 to the icu with j o u r n a l p r e -p r o o f laboratory confirmed covid-19 disease but did not receive any form of plasma therapy. the control group received the usual standard of care as per the national guidelines (ministry of health, oman. human infection with novel corona virus (covid-19)-7. interim guideline for hospitals, primary care and private healthcare, 2020). the control group was matched for baseline characteristics and severity of illness. description of exchange plasma procedure tpe was performed using spectra optia ® apheresis system (termubact, japan), a standard plasma exchange kit (catalog number: 502058310220) and citrate dextrose solution, solution a (acd-a) as an anticoagulant. fresh frozen plasma (ffp) was used as a replacement solution. the total volume of plasma to be replaced was calculated as follows: plasma replacement (l) = body weight (kg) x (1/13) x (100-hematocrit). tpe was performed through a standard femoral central venous catheter (12 fr). each patient underwent a total of five procedures. descriptive statistics were used to describe the data. for categorical variables, frequencies and percentages were reported. differences between groups were analyzed using pearson's 2 tests (or fisher's exact tests for expected cells of <5). for continuous variables, mean and standard deviation were used to summarize the data while analyses were performed using student's t-test. abnormally distributed variables were summarized using median and interquartile range and analyzed using wilcoxon mann-whitney test. statistical analyses were conducted using stata version 16.1 (stata corporation, college station, tx, usa). the study enrolled a total of 31 covid-19 patients fulfilling the who case definition (who clinical management of severe acute respiratory infection when novel coronavirus (ncov) infection is suspected: interim guidance, 25 january 2020, 2020) with an overall mean age of 51  15 years (range: 27-76 years) and 90% (n = 28) were males. a total of 35% (n = 11) of the patients had tpe as a mode of treatment. the three most prevalent comorbidities were diabetes mellitus (48%; n = 15), hypertension (39%; n = 12) and chronic kidney disease (13%; n = 4). both the tpe and the control groups had similar baseline characteristics and underlying comorbidities. the overall median sequential organ failure assessment (sofa) score was 3 (2 -6) for the control group and 6 (3-9) for the tpe group. ninety one percent (n = 10) of the patients in the tpe group had either moderate [pao2/fio2 -200-100] or severe ards [pao2/fio2 -<100], while 50% (n = 10) in the control had either moderate or severe ards. a total of 50% (n =10) of the patients in the control group presented with severe pneumonia. sixty-three percent (n = 19) of the patients had septic shock, 82% (n = 9) in tpe group and 53% (n = 10) in the control group, and 13% (n = 4) had mod, 9.1% (n = 1) in the tpe group and 15% (n = 3) in the control group, respectively. there was a trend for those who were in the tpe group for worse sofa scores and ards, however, the p-values were not statistically significant. those on plasma exchange were less likely to be diagnosed with severe pneumonia than those not on plasma exchange (9.1% versus 50%; p = 0.047). table 1 table 2 outline the clinical outcome characteristics of the cohort stratified by tpe. those on plasma exchange were associated with longer icu length of stay compared to those that were not on plasma exchange (14 versus 6 days; p = 0.028), as they were more seriously ill. additionally, those on tpe were also more likely to be extubated than those not on plasma j o u r n a l p r e -p r o o f exchange (73% versus 20%; p = 0.018). furthermore, patients on tpe had a lower 14 days (0 versus 35%; p = 0.033) and 28 days (0 versus 35%; p =0.033) mortality compared to patients not on tpe . however, all-cause mortality was only marginally lower in the plasma exchange group than those not on plasma exchange (9.1% versus 45%; p = 0.055; power = 66%). clinical indexes, laboratory findings and ventilatory parameters before and after plasma exchange are presented in table 3 . those on tpe generally showed reductions in sofa scores, il-6, crp, d-dimer, and ferritin levels. the novel coronavirus (sar-cov-2) has generated a worldwide attention due to the potential impact on global health. presently, there are no definitive treatments for covid-19 infection and current management strategies focus on supportive care, infection control and investigational therapies. morbidity and mortality from covid-19 infection has been linked to certain risk factors that include: age, prior lung disease, diabetes mellitus, cardiac disease, hypertension, and stroke khamis et al., 2020) . the most prevalent risk factors in our patients were diabetes mellitus, hypertension and chronic renal disease. nearly most of the patients in the plasma group (10/11) presented with moderate to severe ards, while severe pneumonia was the main presentation in the control group. in comparison to the control group, the clinical outcomes were favourable in terms of extubation and mortality benefit with tpe and the effect on the mortality extended up to 28 days (0 vs 35% mortality, p = 0.033). there was also a tendency towards improvement in overall all-cause j o u r n a l p r e -p r o o f mortality, however the sample size was small as denoted by the study statistical power of only 66%. the main causes of death in patients with covid-19 infection were ards and cytokine storm syndrome (felsensteina et al., 2020; huang et al., 2020; qin et al., 2020) . additionally, 50% of patients presenting with cytokine storm syndrome usually develop ards (chen et al., 2019) , thus early recognition and control of dysregulated immune reaction is essential. in severe covid-19 infection, tpe removes toxins and deleterious inflammatory cytokines such as il-1, il-6, granulocyte-colony stimulating factor, tumor necrosis factor and other inflammatory parameters. these inflammatory mediators can trigger a cytokine storm mediated immune injury to the different target organs, resulting in capillary leak syndrome, progressive lung injury, respiratory failure and ards, shock, acute kidney injury and liver impairment (seguin et al., 2016) . simultaneous replacement with normal or convalescent plasma helps to improve hypercoagulable state, reduce cytokine response and replaces adamts13 enzyme (a disintegrin and metalloproteinase with a thrombospondin type 1 motif, member 13). the effect of tpe on the clinical and laboratory parameters was instantly observed following the completion of the 5 cycles (day 7). this included improvement in the sofa scores, increase in the alc and reduction in all inflammatory parameters such as crp, d-dimer, ferritin and il-6. this effect has also been reported elsewhere (shi et al., 2020; zhang et al., 2020) . just over half of our patients in the tpe group and one third in the control group received the il-6 inhibitor; tocilizumab, after plasma exchange and this might additionally have contributed to the decrease in the cytokine storm. however, in a study by xu and colleagues, the j o u r n a l p r e -p r o o f reduction in the inflammatory markers was instant even prior to receiving the il-6 inhibitor (xu et al., 2020) . the use of tpe in the treatment of severe covid-19 infection has shown some positive results, however, the benefit has been limited in macrophage activation syndrome, or sepsis complicated with mods . theoretically, tpe could also remove the formed sars-cov-2 antibodies in addition to the "harmful" dysregulated inflammatory mediators but it remains unclear if there is an antibody response during the cytokine storm or it develops subsequently. the current recommendation of the american plasma exchange association in this regard is as follows "the effectiveness of plasma exchange has not yet been determined and should be individually selected" (winters et al., 2020) . in the implementation of plasma exchange, the key factor in its success is to start tpe in the early stages of covid-19 inflammation and probably when proinflammatory cytokines are high (yang et al., 2020) . in covid-19 patients, it has been reported that the inflammatory cytokines released with severe diseases, including il-6, were significantly higher around 7 to 14 days after the onset of the illness (wan et al. 2020) . thus, early initiation of tpe treatment, within this time frame, could be associated with better outcomes. in our patients, tpe was initiated from 7 days and up to 14 days of illness. it is also necessary to administer tpe for the correct duration and volume, to monitor the potential drug removal of certain therapies such as immunomodulating agents and to practice the proper infection prevention and control measures. tpe is a tolerable procedure by most patients without the occurrence of adverse events, however, the procedure can be a challenge to perform in covid-19 patients who are placed in prone position. earlier studies of the use of plasma j o u r n a l p r e -p r o o f exchange in sepsis has showed that both the timing and disease severity are important for the beneficial effect of tpe (yang et al., 2020) . we routinely performed five tpes daily and noted that respiratory improvements were only seen after completing the therapy on day 7. recognized adverse events related to tpe include allergic reactions, hypotension, hypocalcemia and line related infections. all patients in this case study tolerated tpe except for one episode of hypotension which resolved after normal saline bolus and hydrocortisone injection and did not recur with subsequent procedures. we note that this single-center small trial is not without limitations. it's possible that patients could have improved naturally but the laboratory and ventilatory changes before and after plasma exchange are encouraging for the tpe group. the use of the il-6 antagonist, tocilizumab, could also have contributed to the beneficial effects of tpe. the current study is a case series with small number of patients, a larger well-powered randomized clinical trial is warranted to confirm the beneficial outcomes of tpe. this single-center, case series study on the use of tpe in the management of infection has demonstrated results that are encouraging and support the need for further investigations. based on our experience, tpe should be utilized earlier in critically ill patients with mods and ards within 7 to 14 days of onset of illness. tpe shows promise; however, randomized clinical trials are warranted to draw final conclusive findings. the declare no conflict of interest j o u r n a l p r e -p r o o f j o u r n a l p r e -p r o o f covid-19 pandemic by country and territory a novel treatment approach to the novel coronavirus: an argument for the use of therapeutic plasma exchange for fulminant covid-19 available at sepsis and septic shock: endothelial molecular pathogenesis associated with vascular microthrombotic disease effective treatment of severe covid-19 patients with tocilizumab early safety indicators of covid-19 convalescent plasma in 5,000 patients early therapeutic plasma exchange in septic shock: a prospective open-label nonrandomized pilot study 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covid-19: recommendation and consensus clinical features and treatment of covid-19 patients in northeast chongqing il-6, interleukin 6; crp, c-reactive protein; cll, chronic lymphocytic leukemia; fio2, fraction of inspired oxygen; extub, extubated key: cord-341775-mucatzaa authors: shafi, shuja; dar, osman; khan, mishal; khan, minal; azhar, esam i.; mccloskey, brian; zumla, alimuddin; petersen, eskild title: the annual hajj pilgrimage—minimizing the risk of ill health in pilgrims from europe and opportunity for driving the best prevention and health promotion guidelines date: 2016-06-22 journal: int j infect dis doi: 10.1016/j.ijid.2016.06.013 sha: doc_id: 341775 cord_uid: mucatzaa mass gatherings at religious events can pose major public health challenges, particularly the transmission of infectious diseases. every year the kingdom of saudi arabia (ksa) hosts the hajj pilgrimage, the largest gathering held on an annual basis where over 2 million people come to ksa from over 180 countries. living together in crowded conditions exposes the pilgrims and the local population to a range infectious diseases. respiratory and gastrointestinal tract bacterial and viral infections can spread rapidly and affect attendees of mass gatherings. lethal infectious disease outbreaks were common during hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the ksa into public health prevention and surveillance programs. the ksa provides regular updated hajj travel advice and health regulations through international public health agencies such as the who, public health england, the centers for disease control and prevention, and hajj travel agencies. during the hajj, an additional 25 000 health workers are deployed; there are eight hospitals in makkah and mina complete with state-of-the-art surgical wards and intensive care units made specifically available for pilgrims. all medical facilities offer high quality of care, and services are offered free to hajj pilgrims to ensure the risks of ill health to all pilgrims and ksa residents are minimal. a summary of the key health issues that arise in pilgrims from europe during hajj and of the ksa hajj guidelines, together with other factors that may play a role in reducing the risks to pilgrims and to wider global health security, is provided herein. mass gathering sporting and religious events pose important public health challenges, including the transmission of infectious diseases, exacerbation of non-communicable diseases, and disorders related to climate change. [1] [2] [3] [4] [5] every year, the kingdom of saudi arabia (ksa) hosts the hajj pilgrimage, which is the largest mass gathering in the world held on a recurrent annual basis. 3 the hajj occurs annually from the eighth to the 12 th of dhul al-hijah, the last (12 th ) month of the islamic calendar, and two to three million people perform the pilgrimage during this period. 3 a further seven million complete a 'mini' pilgrimage, known as umrah, outside the hajj period throughout the year. mass gatherings at religious events can pose major public health challenges, particularly the transmission of infectious diseases. every year the kingdom of saudi arabia (ksa) hosts the hajj pilgrimage, the largest gathering held on an annual basis where over 2 million people come to ksa from over 180 countries. living together in crowded conditions exposes the pilgrims and the local population to a range infectious diseases. respiratory and gastrointestinal tract bacterial and viral infections can spread rapidly and affect attendees of mass gatherings. lethal infectious disease outbreaks were common during hajj in the 19th and 20th centuries although they have now been controlled to a great extent by the huge investments made by the ksa into public health prevention and surveillance programs. the ksa provides regular updated hajj travel advice and health regulations through international public health agencies such as the who, public health england, the centers for disease control and prevention, and hajj travel agencies. during the hajj, an additional 25 000 health workers are deployed; there are eight hospitals in makkah and mina complete with state-of-the-art surgical wards and intensive care units made specifically available for pilgrims. all medical facilities offer high quality of care, and services are offered free to hajj pilgrims to ensure the risks of ill health to all pilgrims and ksa residents are minimal. a summary of the key health issues that arise in pilgrims from europe during hajj and of the ksa hajj guidelines, together with other factors that may play a role in reducing the risks to pilgrims and to wider global health security, is provided herein. in light of the huge number of pilgrims from all around the worldof which thousands come from low-income countries with minimal access to healthcare -mixing closely for several days in a difficult terrain, it is remarkable that the majority of pilgrims complete the hajj without experiencing any major health issues. infectious disease outbreaks were common during hajj in the 19 th and 20 th centuries and have been controlled to a great extent, although proactive surveillance of the transmission of potential epidemic threats at hajj is critical to preserving global health security. 3, 5 crush injuries and stampedes, which can pose major risks at mass gatherings, are infrequent during the hajj relative to its size and logistical complexity. a summary of the key health issues that arise in pilgrims from europe during hajj and of the ksa hajj guidelines, together with other factors that may play a role in reducing the risks to pilgrims and to wider global health security, is provided herein. respiratory and gastrointestinal tract bacterial and viral infections spread rapidly and affect almost all pilgrims during hajj. [6] [7] [8] [9] [10] [11] [12] [13] respiratory tract infections -whose spread through coughing and sneezing is exacerbated by the crowded hajj conditions -include community-acquired pneumonia, influenza, and tuberculosis (tb). while bacterial and viral pneumonia are well-documented causes of hospital admission in pilgrims, 13 quantifying the increase in risk of tb transmission is more challenging owing to the longer time period between infection and the development of symptoms. the elderly and those with comorbid diseases such as diabetes are particularly vulnerable to morbidity from respiratory illnesses. acute food poisoning is common during the hajj and is caused by toxins produced by staphylococcus aureus and bacillus cereus. gastroenteritis due to salmonella spp and viruses such as rotavirus and norovirus are common during hajj. 3, 12 factors responsible for increasing the spread of gastrointestinal diseases during hajj include contamination of food through unhygienic preparation, prolonged storage of food, drinking from contaminated water sources, and a shortage of water for hand washing. the risks of dehydration are heightened when hajj occurs during summer months, owing to the extremely hot climate in saudi arabia. 14 other infectious disease risks include meningococcal disease, which caused outbreaks during hajj in the early 2000s owing to overcrowding and high carrier rates of neisseria meningitidis among pilgrims. 3, [15] [16] [17] mosquito species responsible for the transmission of malaria and the arbovirus that causes dengue are present in the ksa, although the country has been classified by the world health organization (who) as a low, geographically restricted malaria transmission area since 2008. 3 historically, infectious diseases were the largest cause of morbidity and mortality during hajj, but non-communicable diseases are now a major burden. 3 many pilgrims both elderly and young have existing non-communicable diseases such as diabetes, hypertension, arthritis, epilepsy, liver and kidney disease, which can be worsened by strenuous hajj conditions or if regular medications are neglected during the spiritual activities. in addition to cardiovascular disease, heat exhaustion and heatstroke are important causes of death; again health-related morbidity is exacerbated when hajj occurs during the summer months. the risk of injury from fires has been reduced since tents were replaced with fibreglass and cooking in tents was prohibited following a fire in 1997. however, risks from stampedes and crush injuries remain due to the overcrowding. as the events of the falling cranes and the stampede in the 2015 hajj illustrate, trauma can be a major cause of injury and death during hajj. furthermore, many pilgrims who walk long distances as part of the rituals invariably are injured by motor vehicles. (table 1) table 1 3 the ksa government employs a well-coordinated, intersectoral approach to the planning, communication, public health, and safety issues of the hajj. 3 during the hajj, an additional 25 000 health workers are deployed; there are eight hospitals in makkah and mina complete with state-of-the-art surgical wards and intensive care units made specifically available for pilgrims. 3 all medical facilities offer high quality of care, and services are offered free to hajj pilgrims to ensure the risks of ill health to all pilgrims and ksa residents are minimal. in terms of preventative measures, in addition to the vaccination requirements described below, measures are put in place to ensure food safety and the ministry of health ensures strict enforcement of the regulation that pilgrims are not allowed to bring fresh food or agricultural products into the country. other coordinated activities include targeted insecticide spraying to control mosquito populations, the distribution of health promotion materials to pilgrims, and electronic surveillance of infectious diseases. 3 the health requirements for pilgrimage to mecca (hajj and umrah) are published annually by the ksa government. information for pilgrims is made available on the saudi arabia ministry of health website. [24] [25] [26] meningococcal vaccine is a prerequisite for all pilgrims; hajj visas cannot be issued without proof of meningococcal vaccination. all adults and children aged >2 years must have received a single dose of quadrivalent a/c/y/w-135 vaccine and must show proof of vaccination on a valid international certificate of vaccination or prophylaxis. children between 3 months and 2 years of age must show proof of vaccination with two doses of meningococcal a monovalent vaccine with a 3-month interval between the doses. hajj pilgrims need to have had the meningococcal vaccine 3 years and 10 days before arriving in saudi arabia. other vaccination requirements for hajj pilgrims entering from specific countries include yellow fever and polio vaccines. the yellow fever vaccine is mandatory for all travellers arriving from countries listed by the who as being a yellow fever risk. polio vaccine is required for travellers arriving from countries that have polio virus circulating, or from countries at high risk of reimportation of polio virus, regardless of age and vaccination status. those who do not have evidence certificates are immunized at the port of entry. 3 the saudi ministry of health recommends seasonal influenza vaccine for those at increased risk, such as the elderly and those with chronic comorbidities. 24 however, there is conflicting evidence about the efficacy of influenza vaccine in protecting hajj pilgrims. 27, 28 pneumonia is among the most common causes of hospital admission during hajj, 14 and thus the prevention of pneumococcal infection is crucial. pneumococcal polysaccharide vaccine is recommended for pilgrims aged 65 years and for younger pilgrims with comorbidities. 29 finally, with regard to measles and rubella vaccines, updating immunization against vaccine-preventable diseases in all travellers is strongly recommended. the prevention and management of threats to global health security and protecting the health and lives of pilgrims requires effective cooperation between numerous agencies within and outside the ksa. 30 the hajj can therefore provide important lessons for setting up and maintaining inter-sectoral collaborations, for example between agencies responsible for health, transport, border control, and environmental health. the value of the hajj experience to planners of mass gatherings in sharing best practices is evident, but lessons can go beyond mass gatherings to inform other areas of public health that require inter-sectoral engagement, such as one health and the control of antimicrobial resistance. the hajj also provides an opportunity for research, not only into all aspects of mass gatherings, but also into faith-based health promotion and electronic disease surveillance capacity building. conflict of interest: all authors have an interest in infectious diseases transmission at mass gatherings. european football championship finals: planning for a health legacy olympic and paralympic games: public health surveillance and epidemiology hajj: infectious disease surveillance and control hajj: health lessons for mass gatherings mass gatherings medicine and global health security emerging respiratory tract viral infections bacteria and viruses that cause respiratory tract infections during the pilgrimage (hajj) season in makkah, saudi arabia respiratory tract infections during the annual hajj: potential risks and mitigation strategies viral respiratory infections at the hajj: comparison between uk and saudi pilgrims influenza and respiratory syncytial virus infections in british hajj pilgrims influenza and the hajj: defining influenza-like illness clinically diarrhea at the hajj and umrah causes of hospitalization of pilgrims in the hajj season of the islamic year sun protection during the hajj massgathering-2013 physiological studies on heat exhaustion victims among mecca pilgrims health at hajj and umra research group. meningococcal vaccine coverage in hajj pilgrims prevention of meningococcal disease during the hajj and umrah mass gatherings: past and current measures and future prospects world health organization. health conditions for travelers to saudi arabia for the pilgrimage to mecca (hajj) middle east respiratory syndrome middle east respiratory syndromeadvancing the public health and research agenda on mers-lessons from the south korea outbreak spread of mers to south korea and china emerging novel and antimicrobial-resistant respiratory tract infections: new drug development and therapeutic options mass gathering medicine: 2014 hajj and umra preparation as a leading example kingdom of saudi arabia: ministry of health saudi arabia: ministry of health saudi arabia: ministry of health influenza vaccine in hajj pilgrims: policy issues from field studies influenza vaccine uptake among british muslims attending hajj prevention of pneumococcal infections during mass gathering mass gatherings medicine: international cooperation and progress key: cord-323332-vu2cre8k authors: luo, yang; he, guo-ping; zhou, jijan-wei; luo, ying title: factors impacting compliance with standard precautions in nursing, china date: 2010-11-10 journal: int j infect dis doi: 10.1016/j.ijid.2009.03.037 sha: doc_id: 323332 cord_uid: vu2cre8k objectives: to evaluate registered nurse compliance with standard precautions and to analyze the factors that affect compliance. methods: study data were collected over a 3-month period from june to september 2007. the survey research method was used. a total of 1500 randomly sampled registered nurses from 18 hospitals in hunan, china completed self-report questionnaires. results: of the 1500 nurses included in the study, 1444 returned valid self-report questionnaires. compliance with standard precautions was found to be low in the surveyed nurses. with a maximum possible score of 80, the quartile range of the overall score for compliance for all nurses was 48.29 (upper quartile score 76.36, lower quartile score 28.07), which was occupied by 64.7% of the participants. the factors most affecting compliance were: standard precautions training (odds ratio (or) 2.17, 95% confidence interval (ci) 1.85–2.55) and knowledge (or 1.94, 95% ci 1.01–3.41), followed by hospital grade (or 1.61, 95% ci 1.79–1.86), presence of sharps disposal box in the department (or 1.43, 95% ci 1.10–3.41), general self-efficacy (or 1.29, 95% ci 1.04–1.59), exposure experience (or 0.69, 95% ci 0.56–0.85), and department in which the nurse worked (or 1.24, 95% ci 1.05–1.46). conclusions: the relevant authorities and hospital infection control department should pay more attention to nurse compliance with standard precautions. standard precautions training should be strengthened and sufficient practical personal protection equipment provided in order to reduce hospital infections and protect the health of patients and medical staff. the standard precautions, proposed by the united states centers for disease control and prevention (cdc) in 1996, are guidelines for reducing the risk of transmission of blood-borne and other pathogens in hospitals. the standard precautions propose that patient blood, body fluid, secretions, and excrement have infectivity, hence isolation measures are necessary. these precautions affect both patients and medical personnel. isolation measures include avoidance of direct contact with patients and air-borne particles, and require hand washing and sterilization, the use of self-protection equipment, the safe disposal of sharp instruments, etc. hospital infections, which pose a serious problem, threatening the health and safety of patients and medical workers worldwide, are infections that arise within the hospital environment. these infections affect the quality of medical care and increase medical care costs. data from the us cdc show that to the end of the year 2002, of 57 medical workers diagnosed with hiv infection following occupational exposure (including 24 nurses), piercing by a sharp instrument had resulted in 48 infections (84.2%). 1 other studies have also shown evidence of clinical nurses becoming infected due to occupational exposure. 2 in a prevalence survey conducted by the world health organization (who) in 55 hospitals across 14 countries, it was found that 8.7% of in-patients acquire infections in hospital. 3 according to mao et al., 4 the incidence of clinic nurses being pierced with sharp instruments potentially contaminated with infected blood is high. they reported the incidence rate of needlestick injury in nurses to be 80.6%. 4 standard precautions protect patients as well as medical workers and help to control the occurrence of hospital infections. as the incidence of infectious blood diseases has increased and with the spread of non-blood infectious diseases such as avian influenza and severe acute respiratory syndrome worldwide, there has been increased emphasis on standard precautions for medical workers, and research into standard precautions has been carried out in many countries. research in this area has mostly been limited to the survey of medical worker knowledge, attitude, and practices. we undertook the current survey, investigating standard precautions knowledge and practice in registered nurses, in order to identify possible corrective factors. this research may provide reference evidence for the associated departments and assist them in instituting policies for preventing nosocomial infections. it may also provide useful information for professional groups formulating training programs to promote the prevention of nosocomial infections. data were collected over a 3-month period from june to september 2007. one thousand five hundred registered nurses in 18 hospitals in four districts of hunan province, china were randomly sampled. among these 18 hospitals, four are first-class hospitals, eight are second-class hospitals, and six are third-class hospitals. participants had to be qualified nurses with over 1 year of working experience in a clinical department and had to be willing to fully cooperate in the survey. those who could not meet the above requirements were excluded from the study. stratified random proportion sampling was adopted in this survey by use of self-report questionnaires. these consisted of four parts and included (1) standard questions to gather participant information, (2) questions pertaining to standard precautions knowledge, (3) questions on compliance with standard precautions, and (4) a general self-efficacy scale. standard precautions knowledge questions were those developed by askarian et al., 5 wang, 6 and li and wang, 7 with modifications. they referred to the basic concepts, content, and activity requirements of the standard precautions, covering 20 items, with possible responses of 'yes', 'no', or 'unknown'. 'yes' is given a value of 1 point, and 'no' or 'unknown' 0 points; the maximum possible score is 20. the higher the score, the greater the knowledge about standard precautions the participant has. the validity of the expertise judgments of the standard precautions questions is 0.98, reliability is 0.86, and cronbach's a is 0.92. compliance with standard precautions was determined using the standard precautions questionnaires developed by askarian et al., 5 wang, 6 and li and wang, 7 with modifications. there are 20 compliance items with a scale of 0-4 points: 0 = never, 1 = seldom, 2 = sometimes, 3 = usually, and 4 = always, giving a score range of 0-80. the higher the score, the better that person carries out the standard precautions. the validity of the expertise judgments of compliance with standard precautions questions is 0.98, reliability is 0.87, and cronbach's a is 0.93. the general self-efficacy scale (gses) used was that originally devised by german psychologist schwarzer and colleagues in 1981; 8 it has been demonstrated to give a good representation of self-efficacy in a variety of settings. 9,10 the scale is a singledimension scale, with 10 questions. each question is assigned points from 1 to 4, and the final score is the average score of the 10 questions. the chinese version, translated by chinese scholars, has been proved to have good validity and reliability; 11 cronbach's a is 0.87 and the test-retest reliability is 0.83, while the correlative factor of items with the full score has a range of 0.60-0.77. 12 the questionnaires were handed out by the investigators (the authors) at each site, and collected on the spot once they had been completed individually and anonymously by the sampled nurses. all data were entered into epidata 3.0 (epidata association, odense, denmark) and processed using spss 13.0 (spss inc., chicago, il, usa) with statistical interpretation of frequency distribution and quartile range. pearson's correlation was used in the analysis of standard precautions knowledge, compliance with standard precautions, and general self-efficacy. multiple linear stepwise regression was adopted to analyze the factors impacting compliance, with a as standard at 0.05 and p as bilateral probability. backward stepwise regression analysis was carried out (a in = 0.05, a out = 0.10). one thousand five hundred registered nurses were surveyed in this study, with a questionnaire return rate of 100%. of the questionnaires, 1444 were valid, giving a rate of 96.3% qualifying questionnaires. the nurses were all female with an average age of 29 ae 7 years and had been working an average of 9 ae 7 years. of the nurses, 60.6% had attended junior college; senior and junior college nurses together accounted for 76.1%. five hundred and seventy-two nurses (39.6%) worked in the internal medicine departments and 647 (44.8%) worked in surgical departments. higher grade hospitals are of a higher general level; of the nurses, 14.4% worked in grade i hospitals, 58.6% in grade ii hospitals, and 27.0% in grade iii hospitals. prior to this survey, most of the nurses had not suffered any injury as a result of piercing with a sharp instrument and had had no experience of exposure to contamination with patient blood, body fluids, secretions, or excretions. half of the nurses were fully qualified and half were not in training. the vast majority of the nurses (93.7%) worked in departments equipped with sharps disposal boxes. with a maximum possible score of 80, the quartile range of the overall score for compliance for all nurses was 48.29 (upper quartile score 76.36, lower quartile score 28.07), which was occupied by 64.7% of the participants. the lowest score was obtained for the use of protection equipment such as eye shields, protective masks, and quarantine clothes. the score was higher for hand washing and sterilization. the score total and scores by item are shown in table 1 . in the analysis, the standard precautions total scores were regarded as dependent variables. participant general information other variables (non-continuous variables) were processed for quantification; among these were sharps injuries and exposure experience (contamination with blood, body fluids, secretions, or excretions of patients), with 0 times scoring 0 points, one time scoring 1 point, two times scoring 2 points, and three or more times scoring 3 points. results are shown in table 2 . the standardized regression coefficients in table 2 show the influence of all the factors impacting compliance -the higher the absolute value the greater the influence on compliance. table 2 shows the results of seven variables: training, knowledge, hospital grade, sharps disposal box in the department, general self-efficacy, exposure experience, and department in which the nurse worked. the standardized regression coefficient for exposure experience was found to be à1.35, suggesting that less exposure experience results in higher compliance to the standard precautions. when testing this regression equation, f = 24.08 (p = 0.00). this shows that the regression equation and the coefficient of standardized regression were significant (p < 0.05). the multiple correlation coefficient r (0 r 1) represents the degree of correlation of multiple impacting factors with activity compliance, with values closer to 1 suggesting a higher degree of correlation. in this investigation, the multiple correlation coefficient r = 0.60, which suggests a high degree of correlation of the above multiple impacting factors with activity compliance. furthermore, the coefficient of determination r 2 (0 r 2 1) represents the percentage of all impacting factors for the explanation of activity compliance. in this investigation, r 2 = 0.36, which shows that the seven factors impacting compliance can interpret 35.7% of the variation in standard precautions. correlation analysis of standard precautions knowledge, general self-efficacy, and compliance with the standard precautions found that standard precautions knowledge was positively correlated with compliance (r = 0.24), suggesting that the greater the standard precautions knowledge the better the activity compliance. general self-efficacy was also positively correlated with compliance (r = 0.21), suggesting that the higher the selfefficacy the better the activity compliance. these results are shown in table 3 . compliance with the standard precautions means that nurses should wash and sterilize their hands, use personal protection equipment correctly, and deal effectively with sharp instruments. the self-report questionnaires adopted for this research collected information on hand washing and sterilization, the use of personal protection equipment, and the disposal of sharp instruments. the scores obtained were similar to those found in the study of li and wang 7 among clinic nurses (from 116 questionnaires) and the study of kermode et al. 13 among healthcare workers in rural north india (from 266 questionnaires), as well as the results of investigations by askarian et al. 5 on the use of standard precautions by clinicians. activity compliance was much higher than that found in the research of shang et al. 14 and wu et al., 15 which may be the result of the different monitoring methods used to study compliance. moreover, shang et al. 14 also found that there was a significant difference between the actual hand washing rate and the self-evaluated hand washing rate. in this investigation, we observed that the use of protective items such as eye shields, masks, and quarantine clothes had the lowest compliance. the use of gloves was higher. in fact, gloves were generally found to be readily available in the departments. reasons given for nurses not using gloves the last time were: the application of gloves will influence the operation (62.6%), too busy to use gloves (19.8%), the patients will complain about the application of gloves (9.9%), gloves are uncomfortable (4.1%), the gloves are not readily available (1.6%), and other reasons (2.0%). in this survey, we also found that most of the clinic departments were not equipped with personal protection items such as eye shields, protective masks, quarantine clothes, and shoe covers. there was relatively higher compliance with hand washing and sterilization and the disposal of sharp instruments. this is mainly related to hospital regulations and repeated education. according to previous investigations, knowledge of standard precautions is lacking in clinicians, nurses, professional personnel involved in infection management, and intern students, as well as other hospital workers. li and zhao 16 investigated the professional personnel involved in infection management in 22 second-class hospitals in luoyang city, and found that 25.0% of them did not understand the concepts of standard precautions. tang et al. 17 investigated 108 nurses in internship, and found that only 16 .7% knew about the standard precautions. xu 18 investigated knowledge of standard precautions in 55 hospital workers; only 32.0% accepted pre-and post-training, only 16.0% of workers knew the indications for hand washing, though none had learned the correct hand washing method, and only 4.0% knew the scope of the standard precautions. askarian et al. 5 investigated medical practitioners at hospitals in iran and found that the median levels of knowledge ranged from 6 to 7 (maximum score 9). monsalve arteaga et al. 19 investigated medical students in venezuela and found a lack of standard precautions knowledge among these students. melo et al. 20 investigated nurses in one hospital in goiania, brazil, and found that only 75.6% understood the standard precautions as protective measures, 52.4% for both professionals and patients and 9.8% for patients with a diagnosed infection. in our survey of 1444 nurses, only half (n = 722) had knowledge of all the standard precautions or had received training. this indicates that half of the nurses had received no education on the standard precautions at all; some had not even heard about them from other sources. this is consistent with the results of other research. in our survey, 98.2% of nurses indicated their wish to be trained in the standard precautions. whether in the univariate analysis or multivariate analysis, knowledge of the standard precautions was found to exert a great impact on the individual's compliance with the precautions (r = 0.24). nurses with standard precautions training had greater precaution compliance than those without standard precautions training. this result is similar to the results found by zhu and chen 12 and vaughn et al. 21 our results indicate that senior staff involved in infection management should gain knowledge themselves and also train their employees. these study results show that knowledge exerts a positive impact on compliance with precautions (or 1.94). this is consistent with the findings of related research by chan et al. 22 in their survey on the standard precautions in nurses, only 48.0% had knowledge of the concepts, 69.0% had knowledge of the objects, and 31.0% had knowledge of the goals of these precautions; this is because hospitals and schools neglect professional protection education. in a large-scale survey carried out by chen 23 involving 17 medical schools, 88.2% of the schools did not provide courses on occupational protection and 22.2% teachers and 27.7% students had no understanding of occupational nursing protection. occupational education pays more attention to basic theory and skills training in medical care and nursing. we found that only 50.0% of nurses had received training on the standard precautions. our results also show the high impact of hospital grade (or 1.61), nurse working department (or 1.24), and presence of a sharps disposal box (or 1.43) on the individual's compliance with the precautions. in this survey, it was found that nurse protection practices in the smaller hospitals were not as good as in the general hospitals. the reason for this may be that smaller hospitals are more basic, lack good infrastructure, and have no specialized infection administration departments. additionally, not enough emphasis is put on the control of hospital infections. in terms of nurse working department, the compliance of nurses in the medical departments was lower than for those in the surgical departments. this difference was found to be statistically significant (p < 0.05), and is probably as a result of the greater number of chronic internal medicine and elderly patients in the medical departments. also, there is no obvious presence of blood in the medical department, which may result in protection being neglected. these results indicate that the administration departments should focus on comprehensive monitoring, especially the monitoring of hospital infections in primary level hospitals. the availability and ease of use of protective equipment are factors that continue to play an important role in compliance with the standard precautions. naing et al. 24 investigated compliance with glove utilization and factors related to non-compliance in hospital universiti sains malaysia, and found that 'stock irregularity', followed by 'gloves not available at the emergency sites', and 'reduction of tactile sensation' were the most important factors impacting compliance. investigations by ferguson et al. 25 into the reasons for non-adherence to standard precautions in community hospitals, showed two related factors -equipment was not available (7%) and the available equipment was not effective (3%). in our survey, it was found that 93.7% of nurses were in departments equipped with sharps disposal boxes; however, when the survey was carried out on location, they did not use these boxes at all. it is known that one-off collection boxes increase department expenses, especially in the grass-roots units. due to economic constraints, protection equipment cannot always be purchased and provided as required by the regulations. using needles with bare hands and the recapping of needles by hand are quite common. this research also shows that sharps injuries and experience of exposure to contamination from a patient 6 months prior to survey exert a great impact on compliance with the standard precautions (or 0.69). it appears that greater compliance with the standard precautions results in less contamination experience. compliance to the precautions in nurses without exposure was found to be greater than in nurses with exposure. this proves that the use of the standard precautions will reduce the chances of occupational exposure. self-efficacy is the core concept of bandura's social cognitive theory, 26 and is the confidence to control and guide ones own activities. schwarzer et al. 9 believe in the existence of general selfefficacy. general self-efficacy is a general confidence when the individual deals with changeable environments and faces new experiences. our research results reveal a positive correlation between general self-efficacy and compliance with precautions (r = 0.21). regression analysis showed general self-efficacy exerts a positive impact on compliance with the standard precautions (or 1.29). these results are consistent with those of the investigations of yang 27 and wang and huang. 28 it is very important to ensure the provision of high quality medical care and security by the prevention and control of hospital infections. nurses play an important role in the prevention and control of hospital infections because they undertake a high proportion of the treatment and care of patients. the standard precautions are a basic measure in the control of hospital infections. results of our research show that compliance with the standard precautions is low in nurses. according to the activity theory model-health belief model, the formation of health beliefs is critical for the acceptance of advice, the correction of misconduct, and the adoption of health activities. most health behavior theories suggest that the most proximal influences on health behavior are attitudinal, social influence, self-efficacy, and intention/stage of change variables. 29 according to our investigation and analysis, the factors impacting compliance with the standard precautions include: standard precautions training and knowledge, hospital grade, presence of a sharps disposal box in the department, general self-efficacy, exposure to patients, and department in which the nurse works. in order to reduce hospital infections and protect the health of patients and medical staff, the relevant authorities and hospital infection control departments should pay more attention to nurse compliance with the standard precautions, strengthen standard precautions training, and provide sufficient practical personal protection equipment. through learning, the attainment of knowledge and skills, and the formation of health beliefs and attitudes, health activity habits can be formed. only when individuals are familiar with the content and meanings of the standard precautions, with strengthening of the individual's health concepts, can individual practice change so as to improve compliance with precautions. in the mean time, hospital infection administration departments should gather more information on hospital infections and provide immediate feedback from the monitoring results in order to strengthen the education and dissemination of the standard precautions among medical workers. for nurses, the study should be strengthened so as to improve concepts of health and general self-efficacy, to increase compliance with the standard precautions and hence reduce the chances of occupational exposure and hospital infection. conflict of interest: no conflict of interest to declare. appendix a surveillance of healthcare personnel with hiv/aids, as of risk of transmission of viral disease by needle punctures and cuts in hospital health care works geneva: world health organization some clinical nurses in the survey needle stick injury knowledge, attitude, and practices related to standard precautions of surgeons and physicians in university-affiliated hospitals of shiraz, iran protection for occupational health investigation standard precaution investigation and the knowledge countermeasures optimistic self-beliefs: assessment of general perceived self-efficacy in thirteen cultures assessment of general perceived selfefficacy on the internet: data collection in cyber space improvement of self-efficacy: an idea and method for clinical nursing appliance of general self-efficacy scale reliability and validity a survey and analysis on status quo of self-protection behavior of nurses in infectious diseases department compliance with universal/standard precautions among health care workers in rural north india a survey and analysis on handwashing of clinical nurses influencing factors in handwashing compliance of nursing staff study on current situation and counter measure of infection management in second general hospitals in luo yang investigation on occupational exposure status quo and guard knowledge in nursing students survey on medical workers' knowledge towards standard precautions and its countermeasures medical students' knowledge and attitude towards standard precautions nurses' understanding of standard precautions at a public hospital in goiania -go factors promoting consistent adherence to safe needle precaution among hospital workers investigating the knowledge, attitudes and practice patterns of operating room staff towards standard and transmission-based precautions: results of a cluster analysis health school nursing education in occupational protection the prevalence of, and factors related to, compliance with glove utilization among nurses in hospital universiti sains malaysia critical incidents of nonadherence with standard precautions guidelines among community hospital-based health care workers self-efficacy: toward a unifying theory of behavioral change the analysis about the health promoting the life form and the interrelated factors of clinical medical persons study on nurses' job burnout and the influencing factors applying health behavior theory to multiple behavior change: considerations and approaches key: cord-347499-7q47jh14 authors: burrel, sonia; hausfater, pierre; dres, martin; pourcher, valérie; luyt, charles-edouard; teyssou, elisa; soulié, cathia; calvez, vincent; marcelin, anne-geneviève; boutolleau, david title: co-infection of sars-cov-2 with other respiratory viruses and performance of lower respiratory tract samples for the diagnosis of covid-19 date: 2020-10-25 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.040 sha: doc_id: 347499 cord_uid: 7q47jh14 objectives: we performed a study during the early outbreak period of coronavirus disease 2019 (covid-19) and the seasonal epidemics of other respiratory viral infections in order to describe the extent of co-infections of severe acute respiratory syndrome coronavirus 2 (sars-cov-2) with other respiratory viruses. a second objective consisted in the comparison of the diagnostic performances of urt and lrt samples for sars-cov-2 infection and to compare diagnostic performances of upper and lower respiratory tract (urt and lrt) samples for sars-cov-2 infection. methods: from january 25(th) through march 29(th), 2020, all urt and lrt samples collected from patients with suspected covid-19 received in the virology laboratory of pitié-salpêtrière university hospital (paris, france) were tested simultaneously for sars-cov-2 and other respiratory viruses. results: a total of 1423 consecutive patients were tested: 677 (47.6%) males, 746 (52.4%) females, median age of 50 [1-103] years. twenty-one (1.5%) patients were positive for both sars-cov-2 and other respiratory viruses. the detection rate of sars-cov-2 was significantly higher in lrt than in urt (53.6% versus 13.4%; p < 0.0001). the analysis of paired samples from 117 (8.2%) patients showed that sars-cov-2 load was lower in urt than in lrt samples in 65% of cases. conclusion: the detection of other respiratory viruses in patients during epidemic period cannot rule out sars-cov-2 co-infection. furthermore, lrt samples increases the accuracy of diagnosis of covid-19. sonia burrel a,b , pierre hausfater c,d , martin dres e,f , valérie pourcher b,g , charles-edouard luyt h,i , elisa teyssou a,b , cathia soulié a,b , vincent calvez a,b , anne-geneviève marcelin a,b , david boutolleau a,b* a ap-hp.sorbonne université, hôpital pitié-salpêtrière, service de virologie, paris, france the severe acute respiratory syndrome coronavirus 2 (sars-cov-2) responsible for coronavirus disease 2019 (covid-19) emerged in wuhan, china, in december 2019 , (zhu et al., 2020 . only few studies reported proportions of sars-cov-2 co-infections with other respiratory viruses, ranging from 0% to 20% (chen et al., 2020; kim et al., 2020; leuzinger et al., 2020; lin et al., 2020a; wee et al., 2020) . furthermore, lower respiratory tract (lrt) samples improve significantly the efficiency of diagnosis compared to upper respiratory tract (urt) samples for non-sars-cov-2 respiratory infections (branche et al., 2014; falsey et al., 2012) . this study, performed during the early outbreak period of (table 1) . among patients negative for sars-cov-2 (n=1122), those positive for other respiratory viruses were statistically younger than those negative (median, 39 versus 52 years, p<0.0001). conversely, among patients positive for sars-cov-2 (n=301), no significant age difference was observed between patients positive for other respiratory viruses and those negative (median, 56 versus 54 years, not significant). among the 21 patients co-infected with sars-cov-2, other respiratory viruses detected were non-sars-cov-2 coronavirus (n=6), influenzavirus (n=5), adenovirus (n=3), rhinovirus/enterovirus (n=3), parainfluenzavirus (n=3), and adenovirus+rhinovirus/enterovirus (n=1). only 4/21 (19.0%) co-infected patients were hospitalized in icu, which was significantly lower than the 113/280 (46.4%) patients infected with sars-cov-2 alone (p=0.020) ( table 1) a total of 1160 urt and 379 lrt samples were collected. the detection rate of sars-cov-2 was significantly higher in lrt (203, 53.6%) than in urt (1160, 13.4%; p<0.0001). paired samples from urt and lrt were obtained from 117 (8.2%) patients. among the 85 patients positive for sars-cov-2, 52 (68.2%) showed concordant positive results in urt and lrt samples ( figure 1a ), but sars-cov-2 load was at least 1 log-higher in lrt than in urt samples for 38 (65%) ( figure 1b in the present study, 7% (21/301) of sars-cov-2-positive patients were co-infected with other respiratory viruses. this co-infection rate is similar to some rates (0% to 6.5%) previously reported (chen et al., 2020; leuzinger et al., 2020; lin et al., 2020a) , but lower than others, up to 20% (kim et al., 2020) . this might be due to different study populations or potential spatiotemporal variations in viral epidemiology. in particular, it is very likely that the lockdown in france, that started on march 17 th and lasted until may 11 th , 2020, had no (or very few) influence on the circulation of respiratory viruses during the present study performed from january 25 th through march 29 th , 2020. in line with previous studies, different types of other respiratory viruses were detected together with sars-cov-2 among co-infected patients, including non-sars-cov-2 coronavirus, influenzavirus, adenovirus, rhinovirus/enterovirus, and parainfluenzavirus (kim et al., 2020; leuzinger et al., 2020; lin et al., 2020a; wee et al., 2020) . patients co-infected with sars-cov-2 and other respiratory viruses did not differ significantly in age and gender from those infected with sars-cov-2 alone, as previously described (kim et al., 2020) . among icu patients, the proportion of co-infected patients was significantly lower than the one infected with sars-cov-2 alone, possibly indicating that co-infection with other respiratory viruses might not worsen the severity of sars-cov-2-associated respiratory disease, in accordance with previous study (wee et al., 2020) . we evidenced the higher efficiency of lrt than urt samples for covid-19 diagnosis, with a significantly higher rate of detection of sars-cov-2 and a 1 log-higher sars-cov-2 load for the majority of infected patients. this discrepancy could be explained, in part, by the variability of the delay between the onset of symptoms and the sampling among patients. however, this higher diagnostic performance of lrt samples for respiratory j o u r n a l p r e -p r o o f 6 infections, including covid-19, has been previously reported (branche et al., 2014; falsey et al., 2012; lin et al., 2020b , wang et al., 2020 . in our study, the proportion of patients positive for sars-cov-2 with discordant results was significantly lower than the one of patients positive for other respiratory viruses with discordant results. those different profiles of compartmentalization of pcr positivity within the respiratory tract may suggest some differences of pathophysiology of sars-cov-2 infection compared to infections by other respiratory viruses. in conclusion, the detection of other respiratory viruses in patients during epidemic period cannot rule out sars-cov-2 co-infection, and lrt samples increases the accuracy of diagnosis of viral respiratory infections, including covid-19. the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. detection of respiratory viruses in sputum from adults by use of automated multiplex pcr epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in wuhan, china: a descriptive study detection of 2019 novel coronavirus (2019-ncov) by real-time rt-pcr yield of sputum for viral detection by reverse transcriptase pcr in adults hospitalized with respiratory illness rates of co-infection between sars-cov-2 and other respiratory pathogens epidemiology of severe acute respiratory syndrome coronavirus 2 emergence amidst community-acquired respiratory viruses co-infections of sars-cov-2 with multiple common respiratory pathogens in infected patients comparison of throat swabs and sputum specimens for viral nucleic acid detection in 52 cases of novel coronavirus (sars-cov-2)-infected pneumonia (covid-19) detection of sars-cov-2 in different types of clinical specimens community-acquired viral respiratory infections amongst hospitalized inpatients during a covid-19 outbreak in singapore: co-infection and clinical outcomes characteristics of suspected covid-19 patients according to respiratory virological findings sars-cov-2 (-) other respiratory viruses icu: intensive care unit; y: years a p<0.0001 (mann-withney u test) b rates of hospitalization in icu only for the patients from pitié-salpêtrière university hospital (n=1167) we thank all healthcare workers involved in the diagnosis and treatment of covid-19 patients in pitié-salpêtrière university hospital (paris, france). key: cord-324295-9c1zxjng authors: bonilla-aldana, d. katterine; jimenez-diaz, s. daniela; arango-duque, j. sebastian; aguirre-florez, mateo; balbin-ramon, graciela j.; paniz-mondolfi, alberto; suárez, jose antonio; pachar, monica r.; perez-garcia, luis a.; delgado-noguera, lourdes a.; sierra, manuel antonio; muñoz-lara, fausto; zambrano, lysien i.; rodriguez-morales, alfonso j. title: bats in ecosystems and their wide spectrum of viral infectious threats: sars-cov-2 and other emerging viruses date: 2020-08-20 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.050 sha: doc_id: 324295 cord_uid: 9c1zxjng bats have populated earth for approximately 52 million years, serving as natural reservoirs for a variety of viruses through the course of evolution. transmission of highly pathogenic viruses from bats has been suspected and linked to a spectrum of emerging infectious diseases in humans and animals worldwide. examples of such viruses include marburg, ebola, nipah, hendra, influenza a, dengue, equine encephalitis viruses, lyssaviruses, madariaga and coronaviruses, involving the now pandemic severe acute respiratory syndrome coronavirus 2 (sars-cov-2). herein, we provide a comprehensive review on the diversity, reservoirs, and geographical distribution of the main bat viruses and their potential for cross-species transmission. j o u r n a l p r e -p r o o f bats have populated earth for approximately 52 million years, serving as natural reservoirs for multiple viruses through the course of their existence 7, 8 . the evolution of their physical, physiological and behavioral characteristics has allowed them to expand to all continents except antarctica, with ecological niches located in urban or rural areas, and especially in caves, mines and some types of foliage 9 . evolutional changes have also determined their current eating patterns and their role within the ecosystem 10 . bats are the only mammals capable of flight; they have nocturnal habits during which they either feed or mate and a layer of short fur that protects them from humidity and cold temperatures 11 . bats belong to the order chiroptera (wings on the upper extremities), with approximately 1,100 species subclassified into two suborders: the megachiroptera and microchiroptera. this classification allows a better understanding of some of their behavioral patterns 8, 12, 13 . bats from the megachiroptera suborder, commonly known as megabats, account for approximately 170 species mainly located in asia, africa and oceania or pacific region ( figure 1 ); their size can vary between 40 and 150 cm with their wings spread, and they weigh 1 kg on average. megabats feed exclusively on fruit, seeds and pollen and their main habitats include caves, mines, trees and some buildings. megachiroptera bats cannot echo localize 8 . the microchiroptera or microbats include over 930 species distributed throughout the entire planet with the exception of some islands and the poles. their size ranges from 4 to 16 cm and feed mostly on flowers and fruit. they possess an echolocation system that allows hematophagous bats to search and capture small prey such as lizards, small mammals, and arthropods. their primary habitats include forests and tropical areas although they are also capable of coexisting with humans in some urban settings 8, 12, 13 . j o u r n a l p r e -p r o o f another notable feature is that microbats can travel long distances of up to 2000 km during migratory season to fulfill their nutritional needs, which is relevant to understand local and intercontinental spread of colonies and coexistence with other animals of the same species. microbats also play a role as pollinators as their feces fertilize and distribute seeds among the areas they inhabit, in addition to serving as plague controllers by feeding on insects, frogs, and rats 8, 14 . bats that coexist within the same geographical area often host common microorganisms 11, 12 . contagion rates depend on contact speed and susceptibility to infections of a specific population 12 . evolutionary processes granted bats with hollow bones to facilitate air maneuvering. this hollowness results in the absence of bone marrow and thus the inability to produce b cells necessary for an efficient immune response, making bats asymptomatic carriers for a long list of viruses 8 . additionally, several species are facultative heterotherms capable of entering profound lethargy during periods of physiological stress to compensate for energy and water deficits, favoring viral persistence 12 . continuous physical contact within bats of the same colony facilitates viral circulation, especially during breeding and migration seasons 15 . the proposed mechanisms of viral transmission between microbats is aerosol release produced by larynx vibrations that occur during echolocation in addition to close contact with other types of secretions such as fecal matter and urine 16 . then, bats carry multiple emerging and reemergin pathogens, especially viral threats ( table 1) . studies from the ecohealth alliance suggest that bats are one of the leading carriers of emerging infectious agents that can potentially affect other mammals, including humans [17] [18] [19] . although the precise reservoir of sars-cov-2 has not been established, a sensible hypothesis is that bats of the genus rhinolophus ferrumequinum could be at fault: chinese studies have reported that sars-cov-2 is very similar to coronaviruses naturally found in bats; however, these viruses are constantly evolving and mutating, making it difficult to pinpoint an exact reservoir ( figure 1 ). since there is no effective treatment or vaccine for covid-19 to date, strong regulations---including isolation, quarantine and social distancing---have been established by many countries in an effort to reduce expansion of the disease given the high person-to-person transmissibility of sars-cov-2, either directly by respiratory droplets with infective particles or indirectly by fluid-contaminated objects. j o u r n a l p r e -p r o o f a study in indonesia identified cov genes in bareback fruit bats, where partial rna-dependent rna polymerase (rdrp) sequences and regions between helicase and rdrp genes were detected and amplified in faeces and tissue samples 22 . another study conducted in zhoushan city, zhejiang province, found that out of 334 bats sampled, approximately 26% were naturally infected with coronaviruses 23 . marburg virus is an rna virus belonging to the filoviridae family (genus marburgvirus) ( further molecular testing conducted on liver, spleen and lung samples of egyptian fruit bat rousettus aegyptiacus reported the presence of marv rna ( figure 1 ). possible routes of transmission include fruit contamination and its consumption by humans or direct contact with bat's infected organs. marv can also spread from human to human through contact with bodily fluids or fomites from sick patients (table 3 ). in humans, the incubation period ranges from 3 to 9 days, and clinical presentation usually involves flulike symptoms, fever between 39 and 40 degrees celsius, conjunctivitis, cramps, cervical lymphadenopathy, and hemorrhagic manifestations. death occurs as a consequence of cardiocirculatory collapse and multiple hemorrhages in the digestive tract and lungs. a study detected a high seroprevalence of antibodies against marburg virus in fruit bats in south africa, with a 19.1% seroconversion rate in recaptured bats 24 ; another study detected marv genome in bats captured in zambia 25 ; and a posterior serosurvey identified filovirus-specific immunoglobulin g antibodies in 71 out of 748 serum samples collected from migratory fruit bats 26 . currently, there is no effective treatment for marv infection other than symptomatic support and rehydration, but some hematologic, immunologic, and pharmacologic actions are under development to improve survival rates. ebola virus also belongs to the filoviridae family and displays a negative-stranded single rna genome. first described in 1976 in the democratic republic of the congo, this notorious virus has decimated populations of gorillas, chimpanzees and humans in africa with mortality rates ranging from 25% to 90% (table 2) . evidence of infection has been reported in three different species of frugivorous bats associated with large outbreaks of ebola hemorrhagic fever in 2014-2015, which later escalated to pandemic proportions resulting in the death of 11,301 people 8, 27 . multiple studies point at bats of the genus myotis as the main reservoir for ebola virus given that these bats carry a copy of viral gene vp35 (table 3) studies in africa analyzed 4,022 blood samples from bats, detecting antibodies against ebola virus in one genus of insectivorous bats and six species of fruit bats 29 . another study conducted in sierra leone identified the complete genome of a new ebola virus, the bombali virus, in free-tailed bats resting inside human dwellings, suggesting potential human transmission 30 . in kenya, researchers also identified the bombali virus in the organs and excreta of free-tailed bats (mops condylurus) 31 . in malaysia, an outbreak in pigs and humans took place between september 1998 and april 1999, affecting 283 people and causing 109 human deaths and the slaughter of more than one million pigs (table 2) . initially, the outbreak was attributed to the japanese encephalitis virus; but later, researchers demonstrated that the causal agent was a virus that belonged to the henipavirus genus, family paramyxoviridae, closely related to the hendra virus. fruit bats (genus pteropus) are the main natural reservoir for nipah virus (niv), while pigs serve as intermediate hosts ( table 3 ). the infection is transmitted from bats to pigs and subsequently from pigs to humans ( figure 1 ). on the island of malaysia, researchers found niv in the urine and saliva of flying foxes (pteropus hypomelanus and pteropus vampyrus). initial circulation of niv likely occurred in late 1997 through contaminated food debris from migrating flying foxes on which pigs fed. fruit bat migration to cultivated orchards and pig farms was a consequence of the lack of fruit during droughts related to el niño phenomenon and wild fires in indonesia. a study conducted in 324 bats (predominantly pteropus, p. vampyrus and p. hypomelanus) from malaysia found that 6.48% had neutralizing antibodies against niv and the virus was subsequently isolated from the urine and fruits consumed by p. hypomelanus. previous human studies showed that most cases had a history of direct contact with live pigs. in humans, the disease can be fatal and is characterized by respiratory and particularly severe neurological manifestations, such as encephalitis and coma. clinical signs in animals may vary, including agitation, spasms, seizures, rapid breathing, and harsh cough. evidence of infection (virus isolation, immunohistochemistry, serology) and neurological involvement has been reported in dogs and horses. transmission studies in australia established that niv could rapidly spread through pigs via oral and parenteral inoculation. neutralizing antibodies were detectable 10-14 days after infection [32] [33] [34] [35] [36] . influenza a viruses (iav) are one of the leading causes of disease in humans, with important animal reservoirs including birds, pigs, and horses that can potentially produce new zoonotic variants (table 2) . (table 3) . notably, small yellow-shouldered bats in central america have been proposed as potential mammalian reservoirs of influenza (figure 1 ). research has shown that bats are susceptible to iav infection. a seroprevalence study identified iav h9 in 30% of fruit bats sampled in africa. bats are believed to have the ability to harbor more genetic diversity of the influenza virus than any other mammal and bird species. j o u r n a l p r e -p r o o f hendra virus, formerly known as equine morbillivirus, is a henipavirus of the paramyxoviridae family for which bats of the genus pteropus serve as main vectors (table 2) . this virus is endemic in australian flying foxes which are currently in danger of extinction and it can be detected in blood, urine, faeces, and fetal and uterine tissue. different studies affirm that hendra virus is horizontally transmitted from bat to bat, but in rare instances vertical transmission has been reported ( figure 1 ). although horses are usually accidental hosts that can contract the virus from these megabats, it has been suggested that the virus could be found in the environment, entering equines through the upper airways and oropharynx. transmission to humans occurs with close contact with infected horses, either through bodily fluids or aerosols; studies have ruled out person-to-person transmission. hendra virus was discovered after an outbreak that killed 20 equines and their trainer in queensland, australia, in 1994 37 . the virus remains viable for approximately four days in bat urine and fruit juice, but fails to survive in temperatures above 37 degrees celsius. the disease has an incubation period of 5-12 days, and its main symptoms are similar to influenza but with a mild, progressive encephalitis. since this infection is uncommon in humans, an effective antiviral has not been developed (table 3) . lyssaviruses are a wide range of pathogens that cause rabies ( table 2 ). the first case of human rabies was reported in ukraine in 1977. hematophagous bat desmodus rotundus, mainly located in latin america ( figure 2) , is considered the primary vector of this disease, which historically has resulted in large economic losses by causing the death of cattle and horses that get infected through bat bites. occasionally, those bites are also seen in human beings (figures 3-4) . lyssaviruses have also been identified in other hematophagous bats such as diphylla ecaudata and diaemus youngi and frugivorous species such as artibeus, planirostris trinitalis, diclidurus albus, hemiderma sp. and phyllostoma superciliatum (table 3) . a colombian study performed on 286 brains from bats of six families and 23 species showed that two species, artibeus lituratus and artibeus planirostris, were positive for the rabies virus 38 . another study conducted in chile reported that 9.5% of 15,000 bats captured were naturally infected 39 as a consequence of the destruction of natural habitats, closer interaction between bats and humans has grown significantly, especially in mining areas 44 . rabies transmission primarily occurs via direct bites or scratches from infected bats 38 ; secondary transmissions in humans takes place through contact with infected pets. these viruses cause acute progressive encephalitis that is inevitably fatal from the onset of clinical signs. initial symptoms are similar to influenza and evolve in a few days to severe neurological involvement that ultimately leads to death 45, 46 . currently, only preventive vaccines are available [47] [48] [49] [50] [51] . dengue virus (denv) belongs to the flaviviridae family, which is transmitted by mosquitoes, most commonly aedes aegypti ( table 2) 52 . there are four denv serotypes (denv-1, denv-2, denv-3 and denv-4) that can cause febrile syndromes in humans. dengue fever is recognized as an epidemic reemerging disease that has affected many countries in recent decades 53-57 . there is evidence that bats could naturally become infected with denv 58 . in mexico, a study evaluated 162 bats and identified denv nucleic acid and anti-denv antibody 59 . another study in costa rica evaluated 12 species of bats, reporting a cumulative seroprevalence of 21.2% (51/241) by prnt and a j o u r n a l p r e -p r o o f prevalence of 8.8% (28/318) in organs tested by rt-pcr 60 . in french guiana, denv nucleic acid was detected in the liver and sera of wild-caught bats 61 . recently in colombia, viral rna was obtained from bat tissues, and a nested-rt-pcr detected amplicons of 143 fragment of the ns5 gene that were then sequenced by the sanger method. in non-hematophagous bats such as carollia perspicillata and phyllostomus discolor captured in ayapel and san carlos (córdoba) respectively, an amplicon corresponding to ns5 was detected; these amplicons showed high similarity with denv-2 57 . yet, the clinical relevance of denv isolation from bats is unclear, as well as the implications in transmission to humans. similarly occurs with other arboviruses, such as madariaga and the equine encephalitis viruses. so far, the have been confirmed as infected hosts, probably reservoirs, but not a direct source for human infections (figure 1 ). the equine encephalitis group involves rna viruses belonging to the togaviridae family, of the alphavirus (table 3 ). these findings suggest that fruit bats from the caribbean region in colombia could be involved in the enzootic cycle of eev 62 (figure 1 ). the madariaga virus is a strain of the eastern equine encephalitis virus. rats and bats presumably serve as the main vectors given the reported seropositivy of brown short-tailed bats (carollia castanea), lanza bats (phyllostomus discolor) and seba's short-tailed bats (carollia perspicillata) 65 . several factors increase the interaction between humans and bats. in most cases, this is due to the intrusion of humans into virgin territories inhabited by bats, fueled by the search of economical resources. this j o u r n a l p r e -p r o o f phenomenon forces bats to adapt to new settings occupied by men, such as buildings, tombs, mines and bridges. additional illegal trading of bats for human consumption and traditional medicine in asia, coupled with poor sanitation and hygiene practices, has facilitated the emergence of zoonotic diseases, some with pandemic potential. financial openness and globalization involve close connections between countries and across continents and can serve as a mean of transportation that accelerates the spread of these emerging diseases. emerging diseases are a global matter of concern, especially during the last decades, and now even more with the occurrence of the 2020 pandemic of covid-19. sars-cov-2 and other emerging pathogens are significantly present in bats. recognizing bats as potential reservoirs or transmission sources for several pathogens that can be a threat to human beings is of upmost importance for global health since many of these conditions may cause severe damage and even 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from sars, mers and recent advances to combat this pandemic virus none. key: cord-345275-h0hvaxgx authors: sun, mengyao; xu, yinghui; he, hua; zhang, li; wang, xu; qiu, qing; sun, chao; guo, ye; qiu, shi; ma, kewei title: potential effective treatment for covid-19: systematic review and meta-analysis of the severe infectious disease with convalescent plasma therapy date: 2020-07-04 journal: int j infect dis doi: 10.1016/j.ijid.2020.06.107 sha: doc_id: 345275 cord_uid: h0hvaxgx abstract background convalescent plasma (cp) has been used successfully to treat many types of infectious diseases, and it has shown initial effects in the treatment of the emerging 2019 coronavirus disease (covid-19). however, its curative effect and feasibility have yet to be confirmed by formal evaluation and well-designed clinical trials. to explore the effectiveness of treatment and predict the potential effect of cp for covid-19, studies of different types of infectious diseases treated with cp were included in this systematic review and meta-analysis. methods related studies were obtained from databases and screened based on the inclusion criteria. the data quality was assessed, and the data were extracted and pooled for analysis. results we included 40 studies on cp treatment for infectious diseases we found that cp treatment could reduce the risk of mortality with a low incidence of adverse events, promote the production of antibodies, show the decline in viral load, and shorten the disease course. a meta-analysis of 15 controlled studies showed that there was a significantly lower mortality rate in the group treated with cp (pooled or = 0.32, 95% ci: 0.19-0.52, p < 0.001, i2 = 54%) than in the control groups. studies were mostly of low or very low quality with a moderate or high risk of bias. the sources of clinical and methodological heterogeneity were identified. the exclusion of heterogeneity indicated that the results were stable. conclusions cp therapy has some curative effect and is well tolerated to treat infectious diseases. it is a potentially effective treatment for covid-19. 3 lead to death in severe cases [1] . the epidemic causing more than 2 million infections and 140 thousand deaths so far has spread quickly worldwide since december 12, 2019 , and the number of infections is gradually increasing throughout the world. to date, there are no approved specific antiviral agents for covid -19, convalescent plasma (cp) therapy has shown some effect and is strongly expected to be used to treat covid -19. the china national biotech group reported on february 13, 2019, that it had detected high titers of virus-neutralizing antibodies as a result of cp. more than 10 patients with severe disease had significantly improved clinical outcomes 12-24 hours after cp transfusion, which is meaningful for the human race in the fight against covid -19. cp therapy is a form of passive immunisation in which antibody-rich blood is collected from recovered patients and then processed to transfuse into other patients. neutralizing antibody is the key effective factor: it blocks the entry of the virus into a cell by binding to the virus and regulates the immun e system to mediate the phagocytosis of immune cells and remove the virus. cp therapy has been effective for treating diphtheria and tetanus since the late 19th century, but the earliest complete record dates back to the outbreak of the spanish influenza pandemic in 1918. later, cp was used to treat ebola, sars, mers, pandemic influenza, and other unexpected major infectious diseases; additionally, some progress has been made in related research [2 -4] . two systematic reviews on respiratory infection revealed a significant reduction in the pool odds of mortality following cp therapy [5, 6] . these experiences raise the hypothesis that use of cp transfusion could be beneficial in patients infected with sars -cov-2. food and drug adminiastrtion (fda) has approved use of cp to treat severe covid-19 patients. [7] however, its curative effect and feasibility have yet to be confirmed in a large clinical trial, and further study is required to develop specific treatment criteria. to predict the potential effect of cp in covid-19, we conducted a systematic review and meta-analysis of different types of infectious diseases treated with cp and further investigated the key points of cp treatment. literature collection according to the literature retrieval strategies recommended by the cochrane collaboration, databases such as pubmed, web of science, embase, and the cochrane library were comprehensively searched for journal papers published from the time the databases were created to march 30, 2020 with the keywords "convalescent plasma", "sars", "mers", "ebola", "h1n1", "h5n1", "h7n9" and "influenza". additionally, the references of selected studies were searched to identify other eligible studies. the included studies were as follows: (i) the population of interest was human subjects of any age or sex who were diagnosed with sars, mers, ebola, influenza, and other epidemic diseases with a laboratory-confirmed or suspected viral etiology. (ii) study designs included randomised controlled trials (rcts), nonrandomised single-arm intervention studies, prospective and retrospective cohort studies, case reports and case series, and studies with no control group. (iii) the intervention measure was convalescent blood products containing cp (iiii) reporting at least one outcome of interest (mortality, symptom duration, hospital length of stay, antibody levels, viral load, adverse events and other specific outcomes of cp therapy). we excluded (i) reviews and guiding documents, including clinical guidelines and expert consensus, (ii) animal or in vitro cell studies, (iii) studies for which the full text was not available, (iiii) and studies with insufficient data on clinical information. two investigators independently screened the titles and abstracts of the retrieved citations and then assessed the full-text manuscripts that were considered potentially eligible. data extraction and quality assessment the following information was extracted from the collected literature: article title, first author's name, year of publication, study methods, number of patients, types of infectious disease, details of treatment and clinical outcomes. the cochrane bias risk j o u r n a l p r e -p r o o f 5 assessment tool version 5.1 was used to assess the quality of ran domised or prospective controlled studies [8] . the newcastle-ottawa scale (nos) was used for other clinical observational studies [9] . the risk of bias in the included studies was independently assessed by two investigators. differences were solved by discussion or through consultation with the senior investigator. meta-analysis was conducted using review manager 5.3 software. the mantel-haenszel method was used to determine the odds ratio (or) and 95% confidence interval (95% ci). we considered p ≤ 0.05 to be statistically significant. the assessment of between study statistical heterogeneity was based on the i 2 statistic. a high value for i 2 (＞50%) indicates heterogeneity, in which case the random effects model was used, and subgroup analysis was performed according to the factors that may be the source of the heterogeneity. in contrast, for i 2 ≤50%, the fixed effect model was recommended. the analysis of sensitivity and the source of the heterogeneity were evaluated by (1) changing the analysis model and (2) screening the included studies to assess the impact of each study on the outcomes. according to the search criteria, a total of 3524 studies were initially selected, among which 40 studies were included. the screening process was shown in figure 1 [17] [18] [19] [20] , 4 studies reported outcomes for 29 patients with avian influenza a (h5n1) [21] [22] [23] [24] , and 15 studies reported outcomes for 1803 patients with spanish influenza a (h1n1) [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] . clinical outcomes of one patient with avian influenza a (h7n9) were reported [40] . one study including 87 patients with diverse severe influenza was found [41] . for infection with j o u r n a l p r e -p r o o f 6 ebola virus, 6 studies reporting outcomes for 583 patients were included [42] [43] [44] [45] [46] [47] . four studies of 31 patients infected with sars-cov-2 was included [48] [49] [50] . there were 2 nonrandomised prospective studies, 1 randomised prospective study, 12 nonrandomised intervention and cohort studies with control groups, and 25 case series and case reports with no control group. supplementary table 1 the risks of bias of the 3 prospective controlled studies were considered to be moderate according to the cochrane collaboration tool, and all of them were at a high risk of bias in allocation concealment and blinding (supplementary table 2 ). supplementary table 3 summarizes the results of the 37 observational studies for which the nos was used for quality assessment. most of the studies had a moderate to high risk of bias, among which the expected absence of random and blinded intervention was the common caveat, and 25 studies were at extremely high risk of bias due to the lack of a control group . a retrospective controlled study on sars-cov showed no deaths in 19 patients who received cp therapy, and there was a statistically significant difference in the case fatality ratio (cfr) compared with the control group (0% vs 23.8% 95% ci, 6 to 42 p=0.049) [10] . cheng et al. reported a cfr of 12.5% in 80 patients who received cp therapy in hong kong, but the sars-related cfr in hong kong was 17% during the same period [11] . no deaths treated with cp were reported in any of the 4 studies that enrolled fewer than 5 patients infected with sars [12] [13] [14] [15] . in the retrospective controlled study conducted b y hung et al. on patients with influenza a (h1n1) pdm09 who underwent cp therapy via an 7 antibody titer higher than 1:160, the multivariate analysis showed that the intervention group had a significantly lower cfr than the control group (20% vs 54.8%, or=0.20; 95% ci, 6 to 69; p=0.011) [17] . in addition, in the 3 small case series or case reports on cp therapy for patients with influenza a (h1n1) pdm09, only 1 death was reported by sang et al. [18] [19] [20] . however, there was no significant difference (95% ci, 52 to 89; p=0.11) between the 2 groups in a case series of patients with avian influenza a (h5n1); 2 of 26 patients received cp therapy, and the cfrs of the intervention group and control group were 0% and 70%, respectively [22] . the absolute reduction of cfr in the cp group was observed in 3 nonrandomised controlled studies on spanish influenza a (h1n1) (6.7% vs 28.3%, p=0.008, 95% ci, 11 to 32; 6.5% vs 25%, p<0.001, 95% ci, 8 to 30; 4.0% vs 30%, p<0.001, 95% ci, 21 to 31) [25, 26, 33, 34] . in a randomised, prospective, phase ii clinical study on cp therapy for severe influenza conducted by john et al, crf was 2% (1/49) in the treatment group, which was lower than 10% (5/49) in the control group, but there was no statistically significant difference between them (p=0.093) [41] . a study of cp therapy for patients with ebola virus showed that the risk of death was 31% in the cp group and 38% in the control group from day 3 to day 16 after diagnosis (rd: -7%; 95% ci: -18 to -4), and the difference was reduced after adjustment for age and cycle-threshold value (rd: -3%: 95% ci: -13 to 8) [42] . another controlled study on ebola virus showed that the cfr was 28% (12/43) in the cp group and 44% (11/25) in the control group. however, there was no significant difference between the intervention and control groups in these 2 studies [43] . mupapa et al. reported 1 death (cfr: 12.5%) in 8 patients with ebola hemorrhagic fever after treatment with convalescent whole blood, while the overall cfr of this epidemic was 80% [44] .no deaths were reported in patients infected with sars-cov-2 using cp therapy. (table 1-2) . viral loads are highly correlated with disease severity and progression [52] .the indicators of viral load were tested before and after cp therapy in several studies. yeh et al. found that the viral loads decreased from 495×103, 76×103 or 650×103 copies /ml to 0 or 1 copy/ml in 3 patients with sars-cov on day 1 after cp transfusion [14] . hung et al. recorded that the viral loads of patients with influenza a (h1n1) pdm09 were significantly lower in the cp therapy group than in the control group on days 3, 5, and 7 after admission to the icu (p=0.001, p=0.02 and p=0.04) [17] . the virus was not detected in the serum of one patient with avian influenza a (h5n1) on day 7 and day 16 after cp therapy [21] . the viral load was reduced by approximately 12 times (from 1 .68×105 to 1.42×104 copies) in another h5n1-infected patient within 8 hours after cp therapy, and no virus was detected within 32 hours [24] . wu et al. reported that no avian influenza a (h7n9) virus was detected in an infected patient on day 4 after cp therapy. however, in randomised controlled trials of cp therapy for multiple severe influenzas, there was no significant difference between the intervention group and the control group regarding the time when no virus was detected [40] . in a controlled study of ebola, the pcr cycle threshold increased by 3.5 cycles on day 1 after cp transfusion (the ct value was inversely j o u r n a l p r e -p r o o f 9 proportional to the viral load) [42] . another study of convalescent whole blood treatment for ebola virus showed that there was a significant difference between the virus quantification at admission and that within the first 24 hours (p<0.01). in the intervention group, the mean ct value was 23.37±5.0 at admission compared with 29.99±5.9 at 24 hours after blood transfusion. in the control group, the mean ct value was 31.97±8.4 at admission vs 31.25±7.5 at 24 hours after admission [43] . kraft × 105 copies/ml to 180 copies/ml 5 days after the completion of cp transfusion and rt-pcr was negative on day 10 after the completion of cp transfusion [49] . a case series of 5 covid patients was reported by shen et al that ct value increased within 1 day after transfusion and became negative on posttransfusion day 1-3 in 3 patients, 2 became negative on day 12 after the transfusion.they also found that sars-cov-2 was still detectable in all 5 patents even though antiviral treatment had been given for at least 10 days, however, viral load decreased and became undetectable soon after cp treatment, which highlight the possibility that cp have contributed to the clearance of the virus. [50] the case reports from korea recorded the ct value of 2 patients with sars-cov-2 before and after cp therapy. in 1 patient, ct value was changed from 24.98 to 33.96 on day 9 after cp infusion, and the viral was negative after on day 15 after cp infusion. similarly, ct value of another patient changed from 20.51 before cp infusion to 36.33 on day 3 after plasma infusion [51] . based on the above results, it can be concluded that cp therapy can reduce the viral load of infectious diseases to some extent (table 1some of the included studies described the level of antibodies after cp therapy but provided no data on the comparison between the intervention group and the control group. yeh et al. reported that sars-cov igg and igm antibodies in patients increased in a timedependent manner and reached a peak on day 3 to day 5 after cp therapy [14] . according to the test of antibody levels of a patient with avian influenza a (h5n1) from hong kong who received cp therapy, specific antibodies to h5n1 appeared between the 7th and 16th days of treatment with cp [21] . zhou et al. also reported that the specific antibodies rose from negative to a titer of 1:40-1:80 within 5 days after cp therapy in one h5n1-infected patient [24] . one patient with avian influenza a (h7n9) was found to have a neutralizing antibody titer of more than 1:80 at discharge on day 16 after cp therapy [40] . a case report of an ebola-infected patient found that igm antibodies increased almost linearly after cp according to a study of cp therapy for sars-cov-infected patients, patients received j o u r n a l p r e -p r o o f 11 cp in the initial 14 days from diagnosis had a better outcome than those received cp after day 14 from diagnosis(58.3% vs 15.6%; p<0.001). the cfr in the two groups was 6.3% and 21.9%, respectively (p=0.08) [11] . another controlled study on sars-cov also showed poor clinical responses in patients who received cp therapy after day 16 [10] . four studies on spanish influenza a (h1n1) showed that early treatment with cp could significantly improve the prognosis, and 2 of the studies provided data showing that patients who received the therapy before day 4 had a lower risk of mortality than those who received the therapy after day 4 (32% vs 60%; 95% ci: 2%-53%; p=0.85 and 14% vs 40%; 95% ci: -2%-72%; p=0.86) [32] [33] [34] [35] [36] [37] . in a study of 16 patients with spanish influenza a (h1n1) who died after cp therapy, the transfusion was provided quite late in 13 patients [39] . based on the above results, it can be concluded that the early use of cp may improve the outcomes of severe infectious diseases (table. 1 -2). a study involving patients infected with sars-cov showed that 74% of patients who received cp were discharged by day 22, compared with 19% in the control group (p=0.001) [10] . zhou et al. reported one case of sars-cov-infected patient recovered within 21 days having a shorter disease course [16] . in a study of ebola virus, the average recovery time was 10.6±3.4 days for patients treated with convalescent whole blood compared with 12.23±4.8 days for the control group [43] . chan et al. reported that the average length of hospital stay after cp transfusion was shorter than that in the control group in 3 patients infected with influenza a (h1n1) pdm09 (36.6 days vs 60 days; p=0.23) [20] . according to the included studies of patients with severe cases and influenza, there were fewer days in the hospital after randomization (median 6 days vs. 11 days, p= 0.13) [41] . to some degree, cp therapy for infectious diseases can reduce the length of hospital stay, shorten the course of disease and contribute to the recovery of patients (table 1 -2). no serious adverse events (sae) related to cp therapy were reported in most of the included studies. according to some relevant stud ies on spanish influenza a (h1n1), the j o u r n a l p r e -p r o o f 12 most common cp-related adverse events were chills and a temporary increase in temperature, which mainly occurs 30-120 minutes after blood transfusion. gould et al. found that the occurrence of jaundice and phlebitis might be associated with blood transfusion [25] [26] [27] [31] [32] [33] [34] [35] [36] [37] . two studies on spanish influenza showed that transfusion might aggravate serious symptoms or hasten death in terminally ill patients [26, 35] . kraft et al. reported that cp transfusion was associated with worsening shortness of breath and increasing oxygen requirements in 1 patient with ebola virus [45] . a case report of one ebola-infected patient had ards possibly caused by transfusion -related acute lung injury, which was managed without mechanical ventilation [46] . a study of severe influenza reported that the incidence of sae was 20% in 42 patients after cp therapy, including ards and stroke [41] . in general, cp infusion is well tolerated, and it is rare to observe serious cp-related adverse events. attention should be paid to terminally patients for exacerbation of the symptoms or disease (table 1 -2). according to the results of the pooled analysis of different types of infectious diseases, cp therapy is effective for reducing the mortality rate and had a significant effect on adjusting the immune system and decreasing the viral load.the synthesis of the length of hospital stay indicates that cp therapy can shorten the course of disease and contribute to patient recovery. the low incidence of serious adverse events, which are mostly controllable, has been shown during and after cp infusion. sars-cov immunoglobulin was prepared successfully using cp in 2004, and it has been approved by the chinese food and drug administration as an emergency rescue drug for the treatment of sars -cov. world health organization (who) has identified cp as a treatment for middle east respiratory syndrome coronavirus (mers-cov), and the international severe acute respiratory and emerging infection consortium (isaric) has recommended cp infusion as a potential treatment for reducing the clinical symptoms of mers -cov infection [53] . in response to sars-cov-2 outbreak, the administration of cp to severe patients was j o u r n a l p r e -p r o o f 13 included in chinese guidelines for the treatment of covid-19 [54] . fda also provided emergency access to for patients with serious or immediately life threatening covid-19 infections [7] . the practice of treating severe infectious diseases with blood products collected from recovered patients reveals the importance of antibodies. the curative effect of cp therapy is attributed to the protective antibodies that block the virus durably and efficiently. it was reported that the immune response is associated with the neutralizing activity of antibodies. after infusion with a 1:80 cp titer in a plaque-reduction neutralization test (prnt), mers-infected patients showed a significant immune response, but the plasma with a prnt titer of 1:40 had no similar response [55] . the patients who had no significant improvement in survival after cp infusion possibly had a lower titer of neutralizing antibodies. therefore, to make the cp more effective, the effective neutralizing antibody titers of cp need to be further explored, and the level of neutralizing antibodies in donor plasma should be determined before transfusion. whether the antibodies in cp are definitely beneficial for treatment is a question. in addition to the complexity of blood products that present risks such as allergic reactions and pathogen transmission, the antibodies probably have a impact on disease severity [56] . the evidence from animal models of sars-cov suggests that the role of antibodies was related to the developement of more severe acute lung injury [57] . studies on the pathogenesis of sars-cov-2 have shown that as the virus attacks the human body, it can trigger a specific immune response; subsequently, a variety of cytokines are produced abundantly. while killing pathogens, cytokines also damage normal tissues and organs in an effect called a cytokine storm. as reported in the clinical data on sars-cov-2 infections in china, cytokine storms are observed in patients with severe disease [58] . there are neutralizing antibodies in cp that prevent the virus from attacking the human body, and nonneutralizing antibodies mainly mediate the virus's entry into macrophages, but when the virus multiplies rapidly in the macrophages, the macroph ages can release excessive pro-inflammatory factors that aggravate the cytokine storm [59, 60] . this may be the explanation that cp therapy worsens the symptoms and hastens the death of j o u r n a l p r e -p r o o f 14 terminally patients with spanish influenza a (h1n1), as well as a potential factor that causes cp-related ards in ebola-infected patients. therefore, we need to be alert for the cytokine storm when applying cp therapy. avoiding the cytokine storm and the reasonable application of cp are the keys for the treatment. the collection and treatment of cp should be performed at the right time to ensure effective antibody titers and boost the patient immune response in the most timely manner. various studies have shown that early treatment with cp resulted in better clinical outcomes than later intervention. there is a 10-day incubation period before the antigen stimulates the primary immune response. later, low-affinity igm and then low-affinity igg antibodies will be produced and will peak on day 21. high-affinity igg antibodies can be produced quickly (in 3-5 days) only as a secondary response [53] . therefore, cp should be given early in the course of the disease, when igg antibodies have not yet been produced in the body. at this time, the passive infusion of high-level and high-affinity igg can improve the humoral immune response, reduce the repeated stimulation of killer t cells in the immune system, avoid cytokine storms, and prevent the disease from worsening or progressing to a critical stage. in china, the collection of blood products is highly regulated. in addition to conventional pathogens and the biological indicator, more than 30 types of pathogens from the respiratory, digestive and urogenital systems were screened in plasma of donors who have recovered from covid-19. furthermore, the process of viral inactivation of plasma is required to ensure the safety of cp [53] . cp collection is an established method in which only plasma is collected, and blood cells are transfused back into the donor. plasma donation has little effect on cured patients, and plasma transfusion is a routine medical procedure. therefore, it is safe and feasible to carry out cp therapy. the present study had several limitations. the lack of high -quality studies was a deficiency of our analysis, and the majority of the included studies were at a moderate to high risk of bias, some of which lacked a control group. the absence of blind intervention in controlled studies promotes this situation. given the limits of database searches and manual retrieval, we cannot be certain that all of the literatures on cp therapy were included, especially reports on spanish influenza from 1918 to 1920. since the record methods of various studies are not unified, some clinical outcomes cannot be analyzed quantitatively. the treatment for infectious diseases is diverse and individualized, and we did not exclude factors that might influence the clinical outcomes, which leads to interference with the evaluation of cp therapy. according to our analysis and prediction, cp has some curative effect and is a safe method to treat infectious diseases early after symptom onset. cp is a potentially effective treatment and can serve as a promising rescue option for severe covid -19 cases. welldesigned clinical trials and further investigation for cp therapy are warranted in the future. the authors declare that they have no confilict of interest. the study does not require ethical approval because the meta-analysis is based on published research and the original data are anonymous. no adverse events were observed with cp in 1 patnent, the fever subsided, and oxygen demand decreased after 1 day of cp transfusion. crp and il-6decreased to normal range on 7day after cp infusion. in another patient, leukocytosis and lymphopenia were immediately recovered after cp infusion.the level of crp and il-6 also recovered to the normal range emerging novel coronavirus (2019-ncov): current scenario, evolutionary perspective based on genome analysis and recent developments convalescent transfusion for pandemic influenza: preparing blood banks for a new plasma product sars: systematic review of treatment effects feasibility, safety, clinical, and laboratory effects of convalescent plasma therapy for patients with middle east respiratory syndrome coronavirus infection: a study protocol meta-analysis: convalescent blood products for spanish inflfluenza pneumonia: a future h5n1 treatment? 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severity, diversity, and transmission clusters of rhinovirus infections the current state of the use of blood plasma for acute infectious diseases during recovery and the prospects of its use for the treatment of novel coronavirus pneumonia diagnosis and treatment plan for novel coronavirus pneumonia (fifth edition for trial implementation).general office of the national health commission challenges of convalescent plasma infusion therapy inm iddle east respiratory coronavirus infection: a single-centre experience current studies of convalescent plasma therapy for covid-19 may underestimate risk of antibody-dependent enhancement anti-spike igg causes severe acute lung injury by skewing macrophage responses during acute sars-cov infection advances in the research of the cytokine storm mechanism induced by coronavirus disease 2019 and the corresponding immunotherapies immune-mediated side-effects of cytokines in humans dysregulated type i interferon and inflammatory monocyte-macrophage responses cause lethal pneumonia in sars-cov-infected mice not applicable. in 4 (57%) of 7 transfusion recipients tested, ebo igg or igm antibodies were present before transfusion (only 2 of them had both igg and igm antibodies). after transfusion, igg and igm antibodies were detected in 7 (87.5%) of the 8 blood key: cord-349418-98sgr5iv authors: bo, yacong; guo, cui; lin, changqing; zeng, yiqian; li, hao bi; zhang, yumiao; hossain, md shakhaoat; chan, jimmy w.m.; yeung, david w.; kwok, kin-on; wong, samuel y.s.; lau, alexis k.h.; lao, xiang qian title: effectiveness of non-pharmaceutical interventions on covid-19 transmission in 190 countries from 23 january to 13 april 2020 date: 2020-10-29 journal: int j infect dis doi: 10.1016/j.ijid.2020.10.066 sha: doc_id: 349418 cord_uid: 98sgr5iv background: to evaluate and compare the effectiveness of four types of non-pharmaceutical interventions (npis) in containing the time-varying effective reproduction number (rt) of covid-19. methods: this study included 1,908,197 confirmed covid-19 cases from 190 countries between 23 january and 13 april 2020. the implemented npis were categorized into four types: mandatory face mask in public, isolation or quarantine, social distancing and traffic restriction (referred to as mandatory mask, quarantine, distancing, and traffic hereafter, respectively). results: the implementations of mandatory mask, quarantine, distancing and traffic were associated with changes (95%confidence interval, ci) of -15.14% (-21.79% to -7.93%), -11.40% (-13.66% to -9.07%), -42.94% (-44.24% to -41.60%) and -9.26% (-11.46% to -7.01%) in the rt of covid-19 compared with those without the implementation of the corresponding measures. distancing and the simultaneous implementation of two or more types of npis seemed to be associated with a greater decrease in the rt of covid-19. conclusion: our study indicates that npis can significantly contain the covid-19 pandemic. distancing and the simultaneous implementation of two or more npis should be the strategic priorities for containing covid-19. the coronavirus disease 2019 , caused by the 2019 novel coronavirus (sars-cov-2), was first reported in wuhan, china, in december 2019. the world health organization (who) declared it as a pandemic on 12 march 2020. as of 28 may 2020, there are more than 5.5 million confirmed cases of 373 related deaths worldwide (word heath organization, 2020). many countries have implemented a series of non-pharmaceutical interventions (npis), such as traffic restriction and social distancing, to contain the outbreak of this disease (jon cohen, 2020, lewnard and lo, 2020) . owing to the rapid transmission of covid-19 worldwide and the lack of an efficient vaccine or treatment for this novel infectious disease, npis are among the few approaches to cope with the resulting pandemic. there is an urgent need to understand whether these npis are effective and which npis are more efficient. however, the information on this topic is limited. most previous studies have focused on evaluating j o u r n a l p r e -p r o o f a single npi within a single city or country using a modelling method, and the results of these studies are inconsistent. few studies have investigated the simultaneous implementation of multiple npis and compared the effectiveness of different npis (lai et al., 2020 , min et al., 2020 . to the best of our knowledge, no study has examined the association between various npis and the time-varying effective reproduction number (rt) of covid-19 on the global scale. therefore, we investigated and compared the effectiveness of four types of npis, namely mandatory face mask in public, isolation or quarantine, social distancing and traffic restriction, on the transmission of in 190 countries between 23 january and 13 april 2020. this ecological study included a total of 415 sites (comprising 235 cities from 10 countries and 180 countries) between 23 january and 13 april 2020. information on the daily number of confirmed covid-19 cases was extracted from a data repository sourced from johns hopkins university center for systems science and engineering and the wind financial database, which archive data from the official websites of health ministries worldwide (dong et al., 2020 , wind, 2020 . data pertaining to the implementation of npis during the study period were obtained from official webpages of or high-circulation newspapers published in the 415 cities/countries. in brief, we first recorded any legal npis announced by the government of each site and its implementation date [i.e. start date and end date (if applicable before the study end date)]. then, we categorized the npis into the following four types: 'mandatory face mask in public' (referred to as mandatory mask hereinafter), 'isolation or quarantine' (referred to as quarantine hereinafter), 'social distancing' (referred to as distancing hereinafter) and 'traffic restriction' (referred to as traffic hereinafter). details pertaining to the process of categorising the npis are summarised in table s1 . if any npi of a type was deemed officially announced as being in force at a site on any day of the study period, that npi type was treated as 'on' for that site on that day in our data j o u r n a l p r e -p r o o f analysis. in contrast, if no npi of a type was found to be effective at a site on any day of the study period, the npi type was treated as 'off' in our data analysis. moreover, we collected demographic and socioeconomic status data for each site. data on population size (number of persons), population density (persons per square km) and median age (years) were obtained from united nations, department of economic and social affairs, population division (elaboration of data by united nations, 2019), and/or statistics bureaus of the countries studied. data on percentages of populations aged 65 years or older were obtained from the world bank data portal (2019 revision). information about the global health security index (ghsi) was collected from the ghs index report.(johns hopkins, 2019) because only country-level ghsi data were available, we applied them to all cities within a given country. we used the rt, which represents the average number of secondary infected cases generated by a primary infected individual at time t, to estimate the changes in covid-19 transmissibility. rt > 1 indicates an expansionary trend of the epidemic, whereas rt < 1 indicates a contractionary trend of the epidemic. we calculated the rt and its 95% credible interval for each day by applying the method developed by cori et al (cori et al., 2013 ) via a 7-day moving average. we assumed that the serial interval distribution of covid-19 followed a gamma distribution with a mean of 3.96 days and a standard deviation (sd) of 4.75 days . first, we used the generalized linear mixed model (glmm) to assess the effectiveness of the four types of npis on the transmission of covid-19 separately. the implementation status (on/off) of each type of npi (i.e. mandatory mask, quarantine, distancing, and traffic) at each site on each day were included in the model as an independent variable. the dependent variable was rt, which was log-transformed to normalize before data analysis and then retransformed to the original scale for presentation. effect estimations were reported as percentage differences in the rt between sites with a given type of npi and sites without the corresponding type of npi j o u r n a l p r e -p r o o f as the reference. a city/country-level random intercept was included in the model to control for clustering effects within the same city/country. two models were developed. model 1 included the following covariates: calendar time to control seasonal and longterm trends over the study period; rt of the previous day to account for temporal autocorrelation; public health response time, which was defined as the number of days between the date of activation of the first npi and the date on which the first case was reported; an indicator for the day of the week and public holidays to account for weekly or periodic variations in the number of people who accepted the sars-cov-2 test; duration for which a type of npi was implemented to control for the potential effects of implementation duration; population density to account for the higher transmission rate in regions with high population density; median age to account for the higher incidence rates among the elderly; and ghsi to account for countries' capacity to prevent and mitigate epidemics and pandemics. model 2 was further mutually adjusted for the other three types of npis, for example, adjusted for quarantine, distancing and traffic to determine the association between the 'mandatory mask' type of npi and rt. second, we compared the effectiveness of the different types of npis implemented. we classified the 415 sites into the following 16 mutually exclusive groups: no implementation of npis; implementation of any one type of npis, namely mandatory mask only, quarantine only, distancing only or traffic only; implementation of any two types of npis, namely 'distancing + mandatory mask', 'distancing + quarantine', 'traffic + mandatory mask', 'traffic + quarantine', 'traffic + distancing' or 'quarantine+ mandatory mask'; implementation of any three types of npis, namely 'distancing + quarantine +mandatory mask', 'traffic + quarantine + mandatory mask', 'traffic + distancing + mandatory mask' or 'traffic + distancing + quarantine'; and implementation of all four types of npis, that is, 'traffic + distancing + quarantine + mandatory mask'. we applied the glmm mentioned above with the same covariates as those used in model 1. the reference group was the 'no implementation of npis'. third, stratified analyses were performed to investigate whether these associations were modified by who regions, population density and ghsi. finally, we performed three sensitivity analyses to examine the robustness of the estimated associations and the lag effects: 1) we used the rt on the third day (lag 3), j o u r n a l p r e -p r o o f the seventh day (lag 7) and the 14 th day (lag 14) as the dependent variable to examine the lag effect; 2) we investigated the associations by excluding hubei province in china, which was a significant outlier in the model; 3) we investigated the associations by adjusting for percentages of populations aged 65 years or older instead of median age to consider the effects of age structure. all data analyses were performed using r 3.6.1 (r core team, vienna, austria). a twotailed p value of < 0.05 was considered statistically significant. a total of 415 sites (i.e. 235 cities from 10 countries and 180 countries) were included in this study. table s2 summarises the relevant information on covid-19 and the npis implemented in the 190 countries during the study period. as of 13 april 2020, 1,908,197 cases of covid-19 infection were reported. the highest number of cases was reported in the united states of america [577,165 (30.25% of the total number of cases reported worldwide)], followed by spain, italy, france, germany, the united kingdom, china, iran, turkey and belgium. table 1 shows the data pertaining to the implementation of npis at the study sites over the study period. no official npis were ever implemented in 382 sites. in many sites, two or more types of npis were ever implemented simultaneously during the study period. the common types of npis or combinations of npi types that were implemented across the sites were 'traffic only' (138 sites), 'traffic + quarantine' (130 sites), 'traffic + distancing' (177 sites), and 'traffic + distancing + quarantine' (218 sites). the implementation durations of each type of npi or each combination of npi types ranged from 4 to 38 days. relatively long median durations of implementation were observed for 'traffic only' (12.5 days), 'distancing + mandatory mask' (16 days), 'traffic + quarantine' (33 days), 'traffic + distancing' (19 days), 'traffic + quarantine + mandatory mask' (38 days), 'traffic + distancing + quarantine' (24 days) and 'traffic + distancing + quarantine +mandatory mask' (37 days). j o u r n a l p r e -p r o o f table 2 presents the associations between each type of npi and the rt of covid-19. the implementations of any type of npi were significantly associated with a decrease in the rt of covid-19. mutual adjustments substantially diluted these associations. the implementations of mandatory mask, quarantine, distancing and traffic were associated with changes of -15.14% (-21.79% to -7.93%), -11.40% (-13.66% to -9.07%), -42.94% (-44.24% to -41.60%) and -9.26% (-11.46% to -7.01%) in the rt of covid-19, respectively, compared with the rt in the sites without the implementation of the corresponding measures. table 3 shows the comparisons of the effectiveness of different npis on the rt of covid-19. 'distancing only' led to a greater decrease in the rt of covid-19 than 'traffic only' and 'quarantine only'. the combinations of other types of npis with distancing were generally associated with a greater decrease in the rt compared with the combinations without distancing. the combinations with more types of npis were generally associated with a greater decrease in the rt. no significant associations were observed for 'mandatory mask only', 'distancing + mandatory mask', 'traffic + mandatory mask', and 'traffic + distancing + mandatory mask'. table 4 , subgroup data analysis generally yielded similar results. the association strengths differed slightly for some subgroups, that is, greater decreases in the rt were observed for the subgroups of 'higher population density' and 'lower ghsi'. no significant associations were observed for some subgroups. tables s3-s5 summarise the results of our sensitivity analyses. the decreased magnitudes in the rts were generally smaller on days lag 3, lag 7 and lag 14 compared with those on the current day (table s3) . similar results were obtained by excluding the outlier province (hubei, china) (table s4) , and by adjusting for percentages of aged≥65 years instead of median age (table s5) . most previous studies have investigated the effectiveness of a single npi rather than a group of npis despite the fact that two or more npis are commonly implemented simultaneously (auger et al., 2020 , chinazzi et al., 2020 , hernandez et al., 2020 , milne and xie, 2020 . the results of our study were consistent with those of the studies that concluded that the implementation of npis was associated with a decrease in transmissibility, such as the studies in mainland china showing that travel restrictions might delay the progression of the covid-19 epidemic by 3-5 days (chinazzi et al., 2020 , tian et al., 2020 and the study in new york showing that wearing a mask could reduce daily deaths by 17%-45% over 2 months (eikenberry et al., 2020) . moreover, two studies reported social distancing to be an effective npi (hernandez et al., 2020 , zhang et al., 2020 . a study conducted in china showed that social distancing and epicentre lockdown might reduce the number of new infection cases by up to 98.9% (zhang et al., 2020) , while another study indicated that social distancing reduced the growth rate of confirmed cases in five countries (austria, belgium, italy, malaysia and south korea) by 52.37% on average (sd 13.37%) (hernandez et al., 2020) . a few studies investigated the effectiveness of multiple npis in china , lai et al., 2020 , milne and xie, 2020 , pan et al., 2020 , europe countries (flaxman et al., 2020) , the united kingdom (davies et al., 2020) , and singapore (koo et al., 2020) . their results showed that the implementation of multiple npis was associated with a reduction in the transmission of covid-19. in contrast, a study conducted in 20 european countries revealed that stay-at-home orders, closure of all non-essential businesses and wearing of face masks in public were not significantly associated with j o u r n a l p r e -p r o o f the incidence rate of confirmed cases (hunter et al., 2020) . it is difficult to directly compare the results of our study with those of previous studies owing to multiple reasons, such as differences in study design and period, targeted populations and transmissibility parameters. moreover, most previous studies used modelling methods to simulate the epidemic with the implementation of npis. in contrast, we used the data published on the official webpages of the governments of 190 countries to provide direct evidence about the effectiveness of npi implementation on covid-19 transmission. nevertheless, our study and most previous studies support the implementation of npis as a measure for containing the global pandemic of covidfew studies have compared the effectiveness of different npis and their combinations for containing covid-19. our results showed that the npi of distancing and its combinations with other npi types are associated with a greater decrease in the rt of covid-19, suggesting that distancing should be adopted as a priority npi for covid-19 containment. this is in line with a modelling study in china, which also suggested that social distancing seemed to have a greater impact on the containment of covid-19 outbreak than travel restrictions (lai et al., 2020) . moreover, our study indicated that the simultaneous implementation of two or more npi types seems to be associated with a greater decrease in the rt of covid-19. in the comparisons of the effectiveness of different npis and their combinations, we found nonsignificant associations for 'mandatory mask only' and the combinations 'distancing + mandatory mask', 'traffic + mandatory mask', and 'traffic + distancing + mandatory mask' (table 3) . nonsignificant associations were also found in some subgroup analyses (table 4) , which were inconsistent with previous studies reporting that face mask was associated with reduced risk of covid-19 infection (cheng et al., 2020 , chu et al., 2020 , eikenberry et al., 2020 . the lack of statistical significance for these associations in our study may be ascribed to the small number of cities or countries that implemented the above npi types and combinations. our study has several important strengths. first, we captured the available data on confirmed cases of covid-19 infection and legal npis implemented from 190 countries, which suggests that our findings are applicable in most countries worldwide. the large sample size allowed us to obtain more stable estimates and conduct a series of subgroup and sensitivity analyses, which generally yielded similar results, indicating that the associations observed in our study are robust. second, we adjusted for a series of important confounders in the model, including socio-demographics and healthsecurity capacities. finally, this study is the first to present a comprehensive and quantitative comparison of the effectiveness of various npis and their combinations at a global scale, which may provide timely evidence for policymakers to adopt appropriate npis in different countries to control the outbreak of covid-19. several limitations should be noted. first, we treated an npi as 'on' in the data analysis if the npi was officially announced as being in force by a government. we were unable to account for the intensity of enforcement and people's compliance, which might have varied across countries and cities. also, contents of each npi at different sties might be somewhat different. however, we included a city-level random intercept that may control the between-city variations in intensity and compliance. second, we considered four types of npis that were legally and officially announced by the governments of countries and cities considered in this study. a few npis, such as knowledge promotion, voluntary isolation, and voluntary wearing a mask were not considered. moreover, some cultural factors, such as personal hygiene, social habits and family size, may influence the spread of covid-19. further investigations are warranted to assess the effects of these factors. third, the information of testing capacities in each site was not available. however, we already adjusted for ghsi which is an important indicator reflecting testing capacity. forth, although our results shows non-significant associations of rt with 'mandatory mask only' and the combinations 'distancing + mandatory mask', 'traffic + mandatory mask', and 'traffic + distancing + mandatory mask', we should interpret with cautions because these estimates came from only a few sites. fifth, because all the cities or countries took action to separate infected persons from uninfected persons at the outset, the effects of not separating infected persons remains unknown. additionally, the effects of different npis may be highly correlated, because they commonly synchronously occurred and were jointly implemented, which may contradict the assumption of independent covariates in glmm model. however, the results could also be affected by other npis if only one type of npis was considered. thus, we gradually introduced two models and presented them separately in table 2 . the two models will allow us to compare the potential influences of additional three j o u r n a l p r e -p r o o f other npis on the effect of an individual npi. furthermore, mutually adjusted for the other three types of npis did not materially affect the conclusion. in conclusion, we found that any type of npi, namely mandatory face mask in public, isolation or quarantine, social distancing and traffic restriction, may reduce the spread of covid-19. social distancing seems more effective than the other three types of npis. the simultaneous implementation of two or more types of npis may be more effective for containing the spread of covid-19. this study is in part supported by environmental health research fund of the chinese university of hong kong (7104946). yacong bo is supported by the phd studentship of the chinese university of hong kong. no ethical approval was required. model 1: adjusted for the calendar time, rt on the previous day, public health response time defined as the time in days between the activation of the first npi and the date of reporting of the first case, an indicator of the day of the week and public holidays, implementation duration of npis, population density, median age, and ghsi. model 2: further mutually adjusted for the other three types of npis, for example, adjusted for quarantine, distancing and traffic in the model for the association between 'mandatory mask' type of npi and rt. traffic + distancing + quarantine + mandatory mask type of npi and rt. b sites with no npi implementation are the reference. adjusted for calendar time, rt on the previous day, public health response time defined as the number of days between 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infectious diseases the effectiveness of social distancing in mitigating covid-19 spread: a modelling analysis estimating the effectiveness of non-pharmaceutical interventions on covid-19 control in korea association of public health interventions with the epidemiology of the covid-19 outbreak in wuhan, china an investigation of transmission control measures during the first 50 days of the covid-19 epidemic in china the impact of social distancing and epicenter lockdown on the covid-19 epidemic in mainland china: a data-driven seiqr model study the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. the authors declare that they have no conflicting interests related to this manuscript.j o u r n a l p r e -p r o o f any one type of npi mandatory mask only (-70.12 to -37.95) n/a: not applicable due to no sites implemented the corresponding type of npis results are presented as percentage differences in the rt with [95% confidence interval (ci)] a sites without the corresponding type of npi as the reference. adjusted for calendar time, rt on the previous day, public health response time defined as the number of days between the date of activation of the first npi and the date of reporting of the first case, an indicator of day of the week and public holidays, implementation duration of a type of npi, population density, median age and ghsi, and mutually adjusted for the other three types of npis, for example, adjusted for quarantine, distancing and traffic in the model for the association between the 'mandatory mask' key: cord-349645-6o8773c5 authors: li, he; xu, xiao-long; dai, da-wei; huang, zhen-yu; ma, zhuang; guan, yan-jun title: air pollution and temperature are associated with increased covid-19 incidence: a time series study date: 2020-06-02 journal: int j infect dis doi: 10.1016/j.ijid.2020.05.076 sha: doc_id: 349645 cord_uid: 6o8773c5 objectives: although the covid-19 is known to cause by human-to-human transmission, it remains largely unclear whether ambient air pollutants and meteorological parameters could promote its transmission. methods: a retrospective study is conducted to study whether air quality index (aqi), four ambient air pollutants (pm(2.5), pm(10), no(2) and co) and five meteorological variables (daily temperature, highest temperature, lowest temperature, temperature difference and sunshine duration) could increase covid-19 incidence in wuhan and xiaogan between jan 26(th) to feb 29(th) in 2020. results: first, a significant correlation was found between covid-19 incidence and aqi in both wuhan (r(2) = 0.13, p < 0.05) and xiaogan (r(2) = 0.223, p < 0.01). specifically, among four pollutants, covid-19 incidence was prominently correlated with pm(2.5) and no(2) in both cities. in wuhan, the tightest correlation was observed between no(2) and covid-19 incidence (r(2) = 0.329, p < 0.01). in xiaogan, in addition to the pm(2.5) (r(2) = 0.117, p < 0.01) and no(2) (r(2) = 0.015, p < 0.05), a notable correlation was also observed between the pm(10) and covid-19 incidence (r(2) = 0.105, p < 0.05). moreover, temperature is the only meteorological parameter that constantly correlated well with covid-19 incidence in both wuhan and xiaogan, but in an inverse correlation (p < 0.05). conclusions: aqi, pm(2.5), no(2), and temperature are four variables that could promote the sustained transmission of covid-19. the outbreak of covid-19 from wuhan china had been officially characterized as a pandemic on 11 th march, 2020 (world health organization, 2020b , which has led to more than 3.5 million subjected infected and 0.24 million dead worldwide as of may 4 th 2020 (world health organization, 2020a) . the causative pathogen of covid-19 has been confirmed as the severe acute respiratory syndrome coronavirus-2 (sars-cov-2) (lu et al., 2020) , which belongs to the coronavirus family and previously caused severe acute respiratory syndrome (sars) (peiris et al., 2004) and the middle east respiratory syndrome (mers) (zaki et al., 2012) . air pollution has been an on-going research focus as it is a major environmental threat to human health. sufficient evidence has tightly linked ambient air pollution to occurrence of numerous respiratory disease, such as copd (ling and van eeden, 2009 ) and asthma (gorai et al., 2016) . moreover, air pollution is also associated with infectious diseases transmission. for example, worsen air quality has also been shown to j o u r n a l p r e -p r o o f increase sars fatality (cui et al., 2003) as well as increased influenza incidence (landguth et al., 2020) . in laboratory condition, van doremalen (van doremalen et al., 2020) has demonstrated a long viability of sars-cov-2 in ambient aerosols, which could be an important source of covid-19 transmission (luo et al., 2020) . however, whether ambient air pollutants are associated with increased incidence of covid-19 in the realistic situation remains largely unknown. previous study indicated that meteorological parameters can affect spread and thrive of multiple virus. for example, ambient temperature and relative humidity are inversely associated with influenza a infection rate in japan (iha et al., 2016) . the coronavirus also exhibited a seasonal oscillation of outbreak, which also suggested a strong association between meteorological parameters and virus transmission and viability (killerby et al., 2018) . moreover, although the epidemiological characteristics of sars-cov-2 is not clear, a recent study predicted sars-cov-2 transmits more efficiently in winter than summer (lipsitch, 2020) , indicating the importance of temperature in covid-19 transmission. however, whether covid-19 transmission is associated with meteorological parameters, at this moment, is not backed by sufficient investigations and robust evidence. in this retrospective study, we attempted to conduct an exploratory analysis looking at the association between environment conditions (including ambient pollutants and meteoroidal parameter) and covid-19 incidence/mortality in wuhan, given a city-wide lockdown and varying pollution/meteorological data throughout the entire study period. in this time-series analysis, covid-19 incidence counts in wuhan and xiaogan were provided by the centers for disease control and prevention (cdc) of hubei province (health commission of the hubei province, 2020). the data used in this study are daily case counts of positive j o u r n a l p r e -p r o o f diagnoses of covid-19 from all reporting sources, including laboratory and clinical diagnoses. covid-19 cases of all ages are included. in total, the covid-19 incidence data for wuhan produced over 35 'clusters' of time series between jan 26 th to feb 29 th in 2020. the daily air quality index (aqi), pm 2.5 , pm 10 , no 2 and co concentration were retrieved from the platform aqi (platform aqi, 2020). five meteorological parameters were retrieved from the database of weather.com (the weather channel, 2020), including daily mean temperature, highest temperature, lowest temperature, sun-rise and sun-set time. daily temperature difference and sunshine duration were calculated based on the difference of highest and lowest temperature and sun rise and set time, respectively. thus, a total of five meteorological parameters were enrolled as independent variables. due to imperfect daily reporting practices, covid-19 incidence number in xiaogan exhibited a data on feb 19 th , which was -15. furthermore, china updated their diagnostic criteria on feb 12 th and 13 th , which resulted in a significant increase of covid-19 incidence cases on these days (han and yang, 2020) . thus, these data were excluded from the current study. all data analyses were used in graphpad prism ® 8.0 (graphpad software, la jolla california usa). first, a descriptive analysis were performed to provide an overview of covid-19 incidence and air quality during the study period. next, we utilized linear regression model to fit the dependent variables (covid-19 incidence) for each independent variable (four ambient air pollutants and five meteorological parameters). as the sars-cov-2 has a median incubation period of 4 days in human (guan et al., 2020) , all independent variables were used to fit daily covid-19 incidence from 4 days later. the statistical tests were two-sided, and p-value <0.05 was considered as statistically significant. table 1 , including the aqi, four ambient air pollutants and five meteorological parameters. the aqi value for wuhan and xiaogan were 63.63 + 4.47 and 71.58 + 5, respectively, both of which were categorized as moderate according to us epa standard (united states environmental protection agency, 2019a). the highest and lowest daily covid-19 incidence were 1,690 cases on feb 16 th and 80 cases on jan 26 th in wuhan, respectively. meanwhile, that of xiaogan were 424 on feb 5 th and 0 on feb 29 th , respectively. we then looked into the correlation between local aqi and covid-19 incidence number in each city ( table 2 , fig 1) . the data showed that aqi was significantly and positively associated with daily covid-19 incidence number in both wuhan (r 2 = 0.13, p<0.05) and xiaogan (r 2 = 0.223, p<0.01), which indicating the important role of aqi in covid-19 transmission. thus, we further studied the association of daily newly diagnosed covid-19 cases with each air pollutant in wuhan (table 2, fig 2) . interestingly, all ambient air pollutants showed positive association with daily covid-19 incidence. among them, no 2 (r 2 = 0.329, p<0.01), pm 2.5 (r 2 = 0.174, p<0.05) and co (r 2 = 0.203, p<0.001) exhibited a statistical significance. next, we studied the correlation between meteorological parameters and covid-19 incidence in wuhan. among five parameters, daily temperature (r 2 = 0.126, p<0.05) and daily lowest temperature (r 2 = 0.143, p<0.05) were predominantly correlated with covid-19 incidence, but both in an inverse correlation. in xiaogan, both pm 2.5 (r 2 = 0.23, p<0.01) and no 2 (r 2 = 0.158, p<0.05) were also apparently associated with covid-19 incidence. moreover, a notable correlation was also observed between the pm 10 and incidence cases (r 2 = 0.158, p<0.05). among five meteorological factors, covid-19 incidence correlated well with the temperature (r 2 = 0.13, p<0.05) and daily sunshine duration (r 2 = 0.407, p<0.01), which were, however, in an inverse correlation. multiple factors could impact viral transmission. for example, influenza viability and activity could be potentiated by ambient air pollutants and some meteorological variables (iha et al., 2016 , landguth et al., 2020 . however, this has not been examined for the sars-cov-2. thus, a preliminary analysis was conducted in the current study to assess the role of air pollution and meteorological parameters on covid-19 transmission. we found that covid-19 incidence was enhanced by increased aqi (decreased air quality), pm 2.5 , and no2 and weakened by temperature. the pm is hazardous due to its complicate composition and strong capacity of air suspension. pm could be divided into coarse and fine particulate matter, whose diameter are less than 10 μm and 2.5 μm, respectively. among various causes of respiratory illness, the pm has been shown to potentiate viral transmissions. for instance, ambient pm 2.5 concentration was prominently correlated with influenza-like illness risk at the flu season in beijing, china (feng et al., 2016) . in a single hospital setting, researchers found that both influenza and respiratory syncytial virus remain airborne for a long time period after they attach to pm, which allows viruses to be transmitted by the airborne route (lindsley et al., 2010) . additionally, viral replication in the respiratory system is enhanced by the negative effect of pm on the human respiratory barrier integrity (xian et al., 2020 , zhao et al., 2018 . however, it remains particularly unclear whether the ambient air pollutant could assist sars-cov-2 transmission. in the current study, the pm 2.5 concentration is correlated with the covid-19 incidence in a positive correlation, which agreed with previous studies. based on these information, we hypothesize that there are pm could potentiate the transmission ability of sars-cov-2 in two ways: 1) pm 2.5 could disrupt the integrity of human respiratory barrier integrity (zhao et al., 2018) . thus, the dysfunctional respiratory barrier are more likely to expose deeper respiratory tissue to foreign pathogens. 2) pm could form condensation nuclei for viral attachment (lee et al., 2014) . due to its relative smaller size, pm 2.5 are more pernicious as it can penetrate the respiratory tract and reach alveoli directly (tellier, 2009 ). since both pm, especially j o u r n a l p r e -p r o o f pm 2.5 concentration, were constantly higher than safety guideline of us epa (united states environmental protection agency, 2019b) in both cities, we believed that pm 2.5 is a stronger factor promoting sars-cov-2 transmission. there are a number of studies demonstrate the adverse health effects of no 2 exposure. for example, short-term increase of outdoor no 2 concentration can significantly increase the risk of upper respiratory tract infection (li et al., 2018) . this phenomenon is was particularly notable in children, as this subpopulation is highly susceptible to no 2 induced lung injury (ghosh et al., 2012 , lin et al., 2013 , moshammer et al., 2006 . viral infection was common after no 2 exposure. according to chauhan et al. (chauhan et al., 2003) , four viruses were frequently detected in no 2 -related respiratory tract infection and coronavirus was one of them. previous study indicated that preceding no 2 exposure can decrease host immunity and thus significantly increase infection risk of cytomegalovirus in mice (rose et al., 1988) . moreover, recovered mice tended to be reinfected after re-exposing to no 2 (rose et al., 1989 ). in the current study, although the no 2 level was constantly lower than the us epa standards (united states environmental protection agency, 2016), our data revealed that covid-19 incidence were highly correlated with the ambient no 2 concentration. this finding agreed to epidemiological studies from other regions of the world (chauhan et al., 2003 , lin et al., 2013 . so far, epidemiological studies had identified at least nine viruses' categories that are capable of infecting respiratory tract (nichols et al., 2008 , pavia, 2011 . although all feature seasonal oscillation of outbreaks, only three viruses show peak incidences in the winter months, which are the influenza, human coronavirus, and human respiratory syncytial virus (killerby et al., 2018 , midgley et al., 2007 . although the epidemiological characteristics of sars-cov-2 is not clear, recent study predicted the sars-cov-2 transmits more efficiently in winter than summer (lipsitch, 2020) , indicating the importance of temperature. these data agreed with our results as temperature seems to decrease the incidence of covid-19, indicating an inhibitory effect of temperature on sars-cov-2 transmission. this phenomenon might be related to life-style as people tend to huddle indoors together during winter season. future study needs to investigate the direct effect of temperature on viral activity as well. other than the pm and no 2 , the data from wuhan also indicated that co have a strong positive effect on sars-cov-2 transmission. however, the data from xiaogan failed to repeat the same result. so far, only a few studies are available concerning the effect of co on viral transmission. for example, su et al.(su et al., 2019) presented that co can increase the risk of influenza-like illness. ali also identified that co had a weak positive association with influenza transmissibility (ali et al., 2018) . we believed our current results could not fully represent the potency of co on sars-cov-2 transmission due to relatively limited study period and location. thus, we cannot conclude the effect of co on sars-cov-2 transmission based on current data. further studies are required to elaborate this issue. the current study has some limitations. first, there are only two cities enrolled, which might result in some results deviation from the exact effect of ambient pollution and meteorological parameters on sars-cov-2 transmission. second, the study period is relative short compared to other epidemiological study. in future study, we will enroll more data from multiple countries and areas to validate the results from current study. in conclusion, we found that aqi, pm 2.5 , no 2 and temperature are four variables that could potential promote the sustained transmission of sars-cov-2. personal protective devices, especially the facial mask, shall be suggested to residents for coronavirus protection in highly polluted regions. these is no conflict of interest in this study. sunshine duration -0.000 + 0.000 0.000 -0.002 + 0.000 *** 0.407 table 2 . the correlation between the covid-19 incidence and three ambient air pollution along with five meteorological parameters jan 26 th to feb 29 th in 2020 in wuhan and xiaogan, china. the data marked with *, ** and *** indicated statistical significance, where p <0.05, 0.01 and 0.001, respectively. ambient ozone and influenza transmissibility in hong kong personal exposure to nitrogen dioxide (no2) and the severity of virus-induced asthma in children air pollution and case fatality of sars in the people's republic of china: an 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increased molecular testing low levels of air pollution induce changes of lung function in a panel of schoolchildren respiratory viruses other than influenza virus: impact and therapeutic advances viral infections of the lower respiratory tract: old viruses, new viruses, and the role of diagnosis online air quality monitoring and analysis platform the pathophysiology of enhanced susceptibility to murine cytomegalovirus respiratory infection during short-term exposure to 5 ppm nitrogen dioxide altered susceptibility to viral respiratory infection during short-term exposure to nitrogen dioxide the short-term effects of air pollutants on influenza-like illness in jinan, china aerosol transmission of influenza a virus: a review of new studies united states environmental protection agency. what are the air quality standards for pm? world health organization. coronavirus disease (covid-19) outbreak situation particulate matter 2.5 causes deficiency in barrier integrity in human nasal epithelial cells isolation of a novel coronavirus from a man with pneumonia in saudi arabia nasal epithelial barrier disruption by particulate matter ≤2.5 μm via tight junction protein degradation the authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper. we want to thank all medical workers for their great contribution and sacrifice during this covid-19 pandemics. we also want to thank the financial support from natural science foundation of liaoning province, china (20180551153).j o u r n a l p r e -p r o o f key: cord-356074-kw8c2fgk authors: oboh, mary aigbiremo; omoleke, semeeh akinwale; ajibola, olumide; manneh, jarra; kanteh, abdoulie; sesay, abdul-karim; amambua-ngwa, alfred title: translation of genomic epidemiology of infectious pathogens: enhancing african genomics hubs for outbreaks date: 2020-08-13 journal: int j infect dis doi: 10.1016/j.ijid.2020.08.027 sha: doc_id: 356074 cord_uid: kw8c2fgk background: deadly emerging infectious pathogens place unprecedented challenge on health systems and economies, especially across africa where health care infrastructures are weak, and poverty rates remain high. genomic technologies have been vital in enhancing the understanding and development of intervention approaches against these, such as ebola, and recently the novel coronavirus disease 2019 (covid-19). discussion: africa has contributed a limited number of sars-cov-2 genomes to the global pool in growing open access repositories. to bridge this gap, the africa centre for disease control and prevention (acdc) is coordinating initiatives across the continent to establish genomic hubs in selected well-resourced african centres of excellence. this will allow for standardisation, efficient and rapid data generation and curation. however, the strategy to ensure capacity for high-throughput genomics at selected genomics hubs should not overshadow the deployment of portable, field-friendly and technically less demanding genomics technologies in all affected countries. this will enhance small scale local genomic surveillance in outbreaks, leaving validation and large-scale approaches at central genomic hubs. conclusion: the acdc needs to scale-up its campaign for government support across african union countries to ensure sustainable financing of its strategy for increased pathogen genomic intelligence and other interventions in current and inevitable future epidemics in africa. deadly emerging infectious pathogens place unprecedented challenge on health systems and economies, especially across africa where health care infrastructures are weak, and poverty rates remain high. genomic technologies have been vital in enhancing the understanding and development of intervention approaches against these, such as ebola, and recently the novel coronavirus disease 2019 . africa has contributed a limited number of sars-cov-2 genomes to the global pool in growing open access repositories. to bridge this gap, the africa centre for disease control and prevention (acdc) is coordinating initiatives across the continent to establish genomic hubs in selected well-resourced african centres of excellence. this will allow for standardisation, efficient and rapid data generation and curation. however, the strategy to ensure capacity for high-throughput genomics at selected genomics hubs should not overshadow the deployment of portable, field-friendly and technically less demanding genomics technologies in all affected countries. this will enhance small scale local genomic surveillance in outbreaks, leaving validation and large-scale approaches at central genomic hubs. the acdc needs to scale-up its campaign for government support across african union countries to ensure sustainable financing of its strategy for increased pathogen genomic intelligence and other interventions in current and inevitable future epidemics in africa. covid-19, africa, gisaid, acdc, genomic hubs. the novel coronavirus disease 2019 (covid-19), a viral outbreak caused by the severe acute respiratory syndrome-coronavirus 2 (sars-cov-2), began in wuhan, china in december 2019 and was declared a public health emergency of international concern on the 30 th january j o u r n a l p r e -p r o o f integrate this into our decision making processes on managing covid-19 outbreak within the continent. this set back is primarily due to limited skillset and infrastructure deficiencies (devex 2020) . till date, only 900 sars-cov-2 genome sequences from 14 african countries are represented out of a total of 62,267 whole-genome sequences uploaded in gisaid (gisaid 2020); an online database for the rapid sharing of most viral genomes, clinical and epidemiological data. africa has recorded approximately 642, 387 cases and close to 10,789 deaths from covid-19 (who 2020a). this significantly outnumber the available african sars-cov-2 genomes, putting the continent at disadvantage in global genetic epidemiology studies of sars-cov-2 and consideration in design of vaccines that would provide broad potency against all virus strains circulating in the continent. the above narrative could be different if each country appreciated the need for genetic data and deliberately empower at least one molecular laboratory involved in covid-19 detection and diagnostics with sequencing technologies. the transition to sequencing viral genomes could adopt cost-effective, easily deployable and portable sequencing platforms with less restricted access to reagents and readily available protocol sharing global networks. it is evident that during an epidemic or a pandemic, most countries close their land borders and airspace to restrict movement and curb the spread of the infectious pathogen. therefore, if viral sequencing platforms are not available in-country, they would have to rely on shipping samples to other laboratories in order to generate sequences. this makes real-time contribution to the global sequences challenging and unrealistic. therefore, while acdc aims for a coordinated, centralised approach for high throughput next-generation sequencing using platforms such as the next-seq and hi-seq, consideration for generation of moderate quality data using miseq, capillary electrophoresis and nanopore technology should be prioritised. this model has been tested in the united kingdom with reported success stories (genomicsengland 2017). lack of concerted financial commitment, skilled personnel and advanced infrastructure are top amongst the many hurdles facing biomedical science research in africa (omoleke et al. 2018; gilbert et al. 2020) . unlike in the global north, capacities are heterogeneous with wide differences between most sub-saharan african countries and south africa for example. moreover, research activities are hardly coordinated across borders, disallowing meaningful continental approaches. this is largely driven by lack of political will and buy-in by various african center for disease control. besides data generating platforms, there is also an acute shortage of expertise in genetic and genomic data analysis and interpretation for translation into public health interventions. this lack of trained human capacity has resulted in heavy reliance on research collaborators and donor funding from the global north for limited quality and valid data outputs. hence, the benefit of using genetic epidemiology data in real-time to inform policy is currently largely unrealistic. the acdc has taken up a continental, coordinated perspective to define strategies that will address some of the challenges impeding derivation of full benefit from currently available technologies that facilitate interventions against sars-cov-2 and future emerging pathogens (acdc 2020). the big picture is the setting up of centralised genomics laboratory hubs, coordinated by the pathogen genomics intelligence institute (acdc 2020). the main goal is to strengthen and link health systems with these institutions for effective surveillance, detection, tracking and monitoring outbreaks before they occur across the continent. to substantiate their effort, illumina, one of the leading genomics companies, has donated $1.4 million in equipment, software, and reagents to the region through the acdc (devex 2020). 7 of already establish centres such as the european and american cdcs to put in place regulation and structures that will facilitate and sustaine cross-border collaborative platforms for more robust epidemic preparedness, readiness and response across the continent in the near future. despite the efforts of africa cdc towards centralised genomic hubs, a situation analysis of continental needs and priority areas in epidemic preparedness and genomic intelligence is required. the current state of institutions, infrastructure and human resources for data generation, management and analysis need urgent attention. in the event of epidemics such as covid-19, genomic data generation for real-time decision making could be enhanced by the adoption and decentralised application of small, portable, easily operated experimental tools such as oxford nanopore technology-minion sequencer, illumina miniseq or the bgi-dnbseq across all countries. these easily deployable, user-friendly field-based technologies were very instrumental in the sequencing of the ebola virus (ebov) during the last outbreak in west and central africa (arias et al. 2016; hoenen et al. 2016; quick et al. 2016) . data generated were useful in strategizing and ensuring the efficacy of interventions, including tracking and stopping the spread of ebov and to evaluate vaccine efficacy. already established genomics hubs strategically located in the four geographic regions (west, east, south and north) of the continent could collate samples from each country for validation and high throughput production of data since they have the requisite technical expertise and infrastructure. in this regard, standardised operating procedures, quality-assured operations, and data curation strategy can be assured and disseminated as well. this can provide the benchmark for future comparative data analysis. to build on its current gains, the acdc should engage in a massive campaign for stronger political commitment from member states in funding genomics as a tool for surveillance and monitoring disease outbreaks. better engagement approaches will enable government buyand ensure the financial strength and sustainability of established genomics institutions towards rapid containment of emerging infectious disease epidemics. union rolls out partnership to accelerate covid-19 testing rapid outbreak sequencing of ebola virus in sierra leone identifies transmission chains linked to sporadic cases strengthening africa ' s ability to ' decode ' the coronavirus the 100,000 genomes project protocol v3 preparedness and vulnerability of african countries against importations of covid-19: a modelling study nanopore sequencing as a rapidly deployable ebola outbreak tool genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding quagmire of epidemic disease outbreaks reporting in nigeria real-time, portable genome sequencing for ebola surveillance the cost and cost trajectory of whole-genome analysis guiding treatment of patients with advanced cancers who ramps up preparedness for novel coronavirus in the african region who. statement on the second meeting of the international health regulations ( 2005 ) emergency committee regarding the outbreak of novel coronavirus a novel coronavirus from patients with pneumonia in china this perspective idea came from the genomics platform weekly laboratory updates discussion for which mao is grateful. the authors declare that they have no competing financial interest or personal relationship that could have impacted their position. this perspective did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. the work did not involve human subjects. key: cord-347907-0nrejsgr authors: alqahtani, amani s.; wiley, kerrie e.; tashani, mohamed; willaby, harold w.; heywood, anita e.; bindhim, nasser f.; booy, robert; rashid, harunor title: exploring barriers to and facilitators of preventive measures against infectious diseases among australian hajj pilgrims: cross-sectional studies before and after hajj date: 2016-02-10 journal: int j infect dis doi: 10.1016/j.ijid.2016.02.005 sha: doc_id: 347907 cord_uid: 0nrejsgr objective: for reasons that have yet to be elucidated, the uptake of preventive measures against infectious diseases by hajj pilgrims is variable. the aim of this study was to identify the preventive advice and interventions received by australian pilgrims before hajj, and the barriers to and facilitators of their use during hajj. methods: two cross-sectional surveys of australians pilgrims aged ≥18 years were undertaken, one before and one after the hajj 2014. results: of 356 pilgrims who completed the survey (response rate 94%), 80% had the influenza vaccine, 30% the pneumococcal vaccine, and 30% the pertussis vaccine. concern about contracting disease at hajj was the most cited reason for vaccination (73.4%), and not being aware of vaccine availability was the main reason for non-receipt (56%). those who obtained pre-travel advice were twice as likely to be vaccinated as those who did not seek advice. of 150 pilgrims surveyed upon return, 94% reported practicing hand hygiene during hajj, citing ease of use (67%) and belief in its effectiveness (62.4%) as the main reasons for compliance; university education was a significant predictor of hand hygiene adherence. fifty-three percent used facemasks, with breathing discomfort (76%) and a feeling of suffocation (40%) being the main obstacles to compliance. conclusion: this study indicates that there are significant opportunities to improve awareness among australian hajj pilgrims about the importance of using preventive health measures. the transmission of infectious diseases is high at mass gatherings such as the annual hajj pilgrimage in makkah, saudi arabia. 1 hajj is the largest annual mass gathering on the planet, with around two to three million people attending from over 180 countries. intense congestion, shared accommodation, air pollution, and compromised hygiene all contribute to the transmission of infections at hajj, most notably acute respiratory infections (aris). 1, 2 hajj presents a public health challenge for saudi arabia, as the authorities need to cater for an increasing number of pilgrims and respond to emerging infections such as the middle east respiratory syndrome coronavirus (mers-cov). 3, 4 it is also challenging for the countries sending pilgrims, since these pilgrims can import epidemic diseases to their home countries upon return. in an effort to reduce the risk of infectious diseases at hajj, an array of preventive measures have been recommended by the saudi arabian ministry of health (moh), which include vaccination and hygiene measures (table 1) . 5 however, studies have demonstrated that vaccine uptake and compliance with hygiene and protective measures are highly variable among pilgrims, 6, 7 and the reasons behind this variability remain unclear. to date few studies have assessed the knowledge, attitudes, and beliefs in relation to preventive measures among hajj pilgrims. a recent qualitative study of australian pilgrims found that considerable misconceptions about preventive measures and the risk of respiratory infections prevail among hajj pilgrims. 8 a french study demonstrated that less than half of pilgrims were aware of social distancing and facemask use as precautions against respiratory infections, 9 but no study has explored the barriers to and facilitators of the uptake of preventive measures. to address these questions, two cross-sectional surveys were conducted among australian pilgrims, one before and one after the hajj 2014, to identify what preventive advice and interventions pilgrims received before travel, and what factors influenced their compliance with these measures while they were there. two cross-sectional self-administered questionnaires were distributed among australian hajj pilgrims aged !18 years in 2014. the first survey was conducted on a group of departing pilgrims approximately 1 month before hajj (pre-hajj study). the second survey was conducted on a second, separate group of pilgrims immediately after their return to australia (post-hajj study). the pre-hajj survey collected data on socio-demographic characteristics, hajj itinerary details, and the receipt of pre-travel advice, including vaccinations. the questionnaire also assessed the pilgrims' knowledge of and attitudes towards preventive measures, and their risk perception of diseases occurring at hajj, including influenza, pneumonia, and blood-borne diseases. the post-hajj questionnaire assessed the actual compliance with infection control measures (such as the use of facemasks, hand disinfectants, and handkerchiefs) during hajj, and the barriers to and facilitators of the use of those preventive measures while at hajj. the surveys were primarily in english, with arabic translations available for those who preferred to complete the survey in arabic. muslims residing in the greater sydney area, new south wales (nsw) were the target population for the study. nsw has the largest muslim population (50%) of any state in australia with the majority living in greater sydney. 10 australian hajj pilgrims aged 18 years and over who were planning to attend the hajj 2014 were eligible for recruitment. potential participants were approached through hajj tour operators. the list of accredited hajj travel agents in australia, including their location/address, was obtained from the saudi arabian embassy in canberra, australia. the selection of participants was based on the number of hajj visas allocated for a given travel agent: travel agents with the highest quota of hajj visas were approached first, and the travel agents who dealt with diverse ethnic groups, including arabs, africans, indians, and malays, were prioritized to ensure a diverse sample. for the pre-hajj survey, departing pilgrims were approached at weekly pre-hajj seminars run by travel agents between august 1 and mid-september 2014. all pilgrims attending the seminars were invited to take part in the study. for the post-hajj survey, a second group of pilgrims (separate to the first) were approached in person at community gatherings and events within weeks of returning home from hajj (between mid-october and the end of december 2014). the study was promoted using a number of methods, including the distribution of brochures at mosques and community centres and by word of mouth. a consecutive sampling plan was used to ensure a sample that was representative of pilgrims residing in nsw. assuming that at least 70% of respondents will have a general knowledge of infection control measures, and considering an error margin of 5% to be acceptable for this anonymous survey, a sample of 323 was considered to be sufficient for this study; assuming a noncompletion rate of the survey of 15-20%, a total of 380 participants were targeted. the sample size of this study represents approximately 10% of australian pilgrims to hajj 2014 (which is approximately 3500). previous works studying the uptake of vaccinations among australian hajj pilgrims showed that a convenience sample of 10% of the target population is sufficient. the data collected were entered into an excel spreadsheet. the statistical analysis was performed using ibm spss statistics version 19.0 (ibm corp., armonk, ny, usa). pearson correlation coefficients and chi-square tests were used to assess variables and determine associations and correlations. univariate factors with p-values of <0.25 were entered into multivariable regression analyses. twotailed p-values of 0.05 were considered statistically significant in the multivariable models. this study was reviewed and approved by the human research ethics committee (hrec) at the university of sydney (project no. 2014/599). a total of 380 respondents agreed to participate in the study, of whom 356 (94%) completed the survey questionnaires. their demographic details are presented in table 2 . eighty-two percent of pilgrims (291/356) were attending hajj for the first time, and the median duration of their stay in saudi arabia was 27 (range 7-40) days. all respondents reported receiving meningococcal vaccine; the majority (83%, 297/356) also received one or more other recommended vaccines (table 3) . factors influencing vaccine uptake are listed in table 3 . being aged >40 years was significantly associated with the uptake of recommended vaccines (odds ratio (or) 2.5, 95% confidence interval (ci) 1.2-4.9, p = 0.01), as was having a university education (or 3.4, 95% ci 1.7-6.7, p = 0.01). approximately two thirds (236/356) obtained 'professional travel health advice' from one or more sources before hajj, including 57% (182/236) from general practitioners (gps), 24% (55/ 236) from a specialist travel clinic, 12% (27/236) from a specific hajj website (e.g., moh website 11 ), and 11% (25/236) from the 'smartraveller' website. 12 of those who received professional pretravel advice, 81% (191/236) reported a positive experience with the advice, while the rest described a negative experience. one third (120/356) did not seek any 'professional travel health advice' before hajj. reasons for not seeking pre-travel advice included not recognizing the need to seek such advice (47%, 56/ 120), preference for other sources, i.e., friends, family members, and travel agents (32%, 39/120), reliance on previous experience/ knowledge (14%, 17/120), and previous negative experience of seeking pre-travel advice (7%, 8/120). being within the age band of 34 to 49 years was the only factor associated with receiving professional pre-travel advice (or 2.5, 95% ci 1.5-4, p = 0.01). additional pre-travel health advice sources were also reported, including hajj travel leaders (66%, 235/356), family members and friends who had previous experience of performing hajj (45%, 161/ 356), and 'general websites' on the internet (17%, 59/356). fortysix percent (164/356) were aware of the annual hajj health recommendations issued by the saudi moh. additionally, pilgrims who sought pre-travel advice from gps (or 1.9, 95% ci 1-3.5, p = 0.03) or tour group leaders (or 2.1, 95% ci 1.1-3.8, p = 0.01) before travelling to hajj were twice as likely to be vaccinated as those who did not. pilgrims were reportedly concerned about food poisoning (61%, 217/356), diarrhoea (59%, 210/356), influenza (58%, 206/356), blood-borne diseases (49%, 173/356), skin diseases (45%, 160/356), and pneumonia (33%, 117/356). however, there was no association between the level of concern about influenza, pneumonia, and blood-borne diseases and the uptake of the influenza, pneumococcal, and hepatitis b vaccines, respectively (all p-values >0.2). a total of 150 returned pilgrims were surveyed. their demographic characteristics are presented in table 2 . a large proportion of pilgrims (79%, 118/150) had performed hajj for the first time. they had stayed for a median duration of 25 (range 7-35) days. the majority of participants, 71% (107/150), believed hand washing (with water only) to be the most effective measure to protect oneself from respiratory infections, while the uses of alcoholic hand rubs (37%, 56/150) and facemasks (35%, 52/150) were considered to be less effective. only beliefs about the effectiveness of facemasks and hand washing with water and soap were significantly associated with their actual use (p < 0.01) ( table 4 ). half of the pilgrims (53%, 80/150) used facemasks to protect themselves from infectious diseases during hajj at least three times a day. participants described three major reasons for facemask use: protection from disease (76%, 61/80), protection from air pollution (58%, 46/80), and belief that facemasks are effective in preventing aris (41%, 33/80). less than half (47%, 70/ 150) did not use a facemask. the reasons for non-compliance were breathing discomfort (76%, 53/70), feeling of suffocation (40%, 28/ 70), and thinking it was not necessary (31%, 22/70). in addition, none of the demographic characteristics were associated with facemask compliance (all p-values >0.25) and therefore these were not entered into multivariable regression analyses. a subgroup of women (n = 76) answered questions on their use of the niqab (traditional face veil); of those who responded, 49% (37/76) used only facemasks, 34% (26/76) used only the niqab, and 20% (15/76) used both a facemask and the niqab. of those who used the niqab (either alone or with a facemask), 51% (21/41) reported that they did so because it is 'airy' and easier to breathe and 39% (16/41) felt that it was comfortable to use. almost all (94%, 141/150) practised some kind of hand hygiene during hajj. this included hand washing with soap (73%, 110/150), hand washing with water only (55%, 82/150), and alcoholic hand disinfectant (31%, 46/150). reasons influencing the pilgrims' decision to use these methods included belief in the effectiveness of hand hygiene in preventing infectious diseases (67%, 94/141) and convenience and ease of use (62.4%, 88/141). additionally, those with a university education were more likely to use hand hygiene measures than those without (or 7.9, 95% ci 1.4-42.9, p = 0.01). respondents reported using other preventive measures including disposable handkerchiefs (53%, 79/150), avoiding dense crowding (29%, 43/150), avoiding contact with symptomatic people (39%, 58/150), and practicing hand washing after touching the ill (30%, 45/150). this appears to be the first in-depth quantitative study comparing the health knowledge attitudes, beliefs, and practices of departing and returning hajj pilgrims regarding preventive measures against infectious diseases. this study found that 14 and france where the vaccination rate for 2014 was zero due to vaccine non-availability, 15 and compares well with the overall vaccination rates among international pilgrims over recent decades, which range between 0.7% and 100%. 6, 16 influenza vaccine aside, the uptake of other recommended vaccines was low. for instance, the uptake of pneumococcal vaccine was only 30%. previous australian and international surveys have reported coverage rates ranging from 2.5% to 36%. 6, 17 this is concerning because pneumonia is the leading cause of hospital admission and an important cause of mortality at hajj. [18] [19] [20] furthermore, surveys have shown that many pilgrims were not aware that pneumonia is transmissible 21 and preventable by vaccination. 22 there is currently no formal guidance from the saudi moh on the use of pneumococcal vaccine for hajj pilgrims, which may partly explain this apparent lack of awareness (table 1) . 23 the uptake of pertussis vaccine was 30%, compared with 10.6% among french hajj pilgrims in 2005. 24 additionally, the coverage for hepatitis a and b vaccines were each 17%, which is higher than the 11.5% uptake for hepatitis a reported among french pilgrims in 2005, 24 and the 6% each for hepatitis a and b among saudi pilgrims in 2010. 25 while a large proportion of hajj pilgrims are from countries with intermediate to high hepatitis b virus (hbv) prevalence, the risk of contracting hbv at hajj is not well studied. 26, 27 it is known that a significant proportion of pilgrims engage in high-risk behaviours; for example it was found that about 43% of male pilgrims shaved their heads with reused razors, 28 or had their heads shaved by non-professional (unlicensed) barbers. 25 other studies have also reported high-risk behaviours that increase the risk of hepatitis a, including buying and eating food from street vendors. 29 despite this, hepatitis a and b vaccines are not listed in the saudi moh recommendations for hajj pilgrims (table 1) . 23 in this study, polio vaccine uptake was 8%, which is low compared with the uptake among french pilgrims in 2006 (15%), 30 and the uptake among pilgrims from other non-endemic countries in 2013 (43%). 31 typhoid vaccine coverage was 13% in this study, which compares well with the uptake rate of 9% among international pilgrims in 2002. 32 the present study appears to report mmr (measles, mumps, and rubella) vaccine uptake (10%) for the first time. the participants cited several reasons for not receiving the recommended vaccines, the most common being that they were unaware that the vaccines were recommended. these results are consistent with the findings of memish et al., who reported a lack of knowledge to be a significant factor for poor uptake of the seasonal influenza vaccine among pilgrims. 33 conversely, previous australian studies have reported reliance on natural immunity as the main reason for not being vaccinated against influenza in 2011, while low risk perception of contracting influenza was the main reason in 2012. 13 a unique finding of this study is that pilgrims who received pretravel advice from gps and hajj tour group leaders were twice as likely to be vaccinated as those who did not receive such advice. barasheed et al. found that receiving advice from hajj group leaders was the main motivator for the uptake of influenza vaccine among australian hajj pilgrims in 2012. 13 this survey also revealed that older pilgrims (aged >40 years) were more likely to take up the recommended vaccines. similarly, gautret et al. demonstrated that influenza vaccine coverage increased with age in french pilgrims. 24 this could be due to the fact that older people are more aware of their health, or it could be due to an increasing number of pre-existing illnesses as people age. another study among french pilgrims found that 'at risk' pilgrims were significantly more likely to be advised to receive pneumococcal vaccine than those who were not 'at risk'. 22 this may explain why vaccine uptake has been found to increase with age in some studies. 24, 34 although respiratory infections are the most common diseases during hajj, 1 the participants in this study were more concerned about food-borne illness than aris. limited knowledge and perception of diseases among pilgrims has been found in other studies; an australian study found that 42% of pilgrims in 2014 were not aware that pneumonia can be transmissible. 21 similarly, french pilgrims in 2014 did not perceive pneumonia as a severe condition, and were not aware of the existence of a vaccine against it. 22 no association was found between the disease risk perception for influenza, pneumonia, and hepatitis b and the uptake of the respective vaccines. this contradicts other data, which demonstrated that an increased risk perception of pandemic influenza a (h1n1) was significantly associated with influenza vaccine uptake among us pilgrims in 2009. 35 almost all of the participants in the present study used some kind of hand hygiene; this was higher compared with french pilgrims in 2013 (50%). 36 more than half of the pilgrims used facemasks in this study, similar to french pilgrims in 2013. 36 nevertheless, previous studies have reported that only half of the participants were aware of the availability of non-pharmaceutical preventive measures against respiratory infections. 9, 33 belief that hand hygiene is easy to use and effective in preventing infections were the main reasons for uptake among the present sample. conversely, facemasks were less accepted. among non-users, discomfort and difficulty in breathing were barriers to their use. those who used facemasks believed that they were effective in preventing infectious diseases. similar quantitative findings have been reported among members of the general singaporean community, 37 but not previously among hajj pilgrims. another important factor identified as a driver for the use of facemasks was protection from air pollution. a recent study found that the air pollution level in makkah during the hajj consistently exceeds internationally acceptable standards, 38 and therefore this perception is probably justified and could inform health promotion policy. thirty-four percent of female pilgrims in the present sample preferred to use a traditional face cover (niqab) to a facemask during hajj. in contrast, other studies found that higher proportions (over 70%) of saudi women preferred the niqab over facemasks at hajj 2002 and 2003. 39, 40 in the exploration of why some women prefer using the niqab, it was found that comfort and breathability were contributing factors. in this study, two thirds of pilgrims sought pre-travel advice from health professionals; this is similar to the results of a survey that found that 65% of arab pilgrims received health advice before departing to hajj. 41 gps were the most cited sources, followed by specialist travel clinics. this result is supported by a study that found gps to be the most trusted sources of health advice among australian pilgrims in 2014. 21 interestingly, only 12% of the present sample sought advice from the saudi moh website. this is different to the findings of a study that showed the saudi moh to be the main source of health information among pilgrims from arab countries (69%). 41 this difference may be due to language barriers. not recognizing the need to seek pre-travel health advice and the preference for other information sources (i.e., friends, family members, and travel agents) were the main barriers to seeking professional pre-travel advice. these results support the findings of a recent australian study, which also demonstrated a high level of confidence in advice from non-health professional sources such as family, friends, and travel agents. 8 the present study identified that being aged between 34 and 49 years was the only factor significantly associated with seeking pre-travel health advice. therefore, enhancing awareness among other groups of hajj pilgrims, especially elderly adults and those with pre-existing illnesses, about the importance of seeking professional pre-travel advice could be an important strategy to improve the uptake of preventive measures. moreover, providing gps with culturally appropriate health information on hajj and the preventive measures recommended by the saudi moh could also facilitate uptake. 42 this study has some limitations. two different groups were surveyed and the groups showed significant differences in demographic characteristics, particularly in sex, education level, and country of birth. also, the sample size of the post-hajj group was smaller than intended. these could limit the generalizability of the findings of one group to the other. these limitations are being addressed by a second, larger cohort study among australian pilgrims during hajj 2015, and a qualitative study among gps and tour group leaders is underway. despite these limitations this study has uniquely identified the barriers to and facilitators of the uptake of preventive measures among australian hajj pilgrims, providing important preliminary data upon which to build. this study shows that there are significant opportunities to improve awareness among hajj pilgrims about the importance of using preventive health measures and indicates the need for better communication of official health information from the saudi moh to a broader international audience. conflict of interest: professor robert booy has received funding from baxter, csl, gsk, merck, novartis, pfizer, roche, romark, and sanofi pasteur for the conduct of sponsored research, travel to present at conferences, or consultancy work; 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